##############################################################################
##############################################################################
###
### Running command:
###
### rm -rf LEA.buildbin-libdir LEA.Rcheck && mkdir LEA.buildbin-libdir LEA.Rcheck && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=LEA.buildbin-libdir LEA_1.8.1.tar.gz >LEA.Rcheck\00install.out 2>&1 && cp LEA.Rcheck\00install.out LEA-install.out && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD check --library=LEA.buildbin-libdir --install="check:LEA-install.out" --force-multiarch --no-vignettes --timings LEA_1.8.1.tar.gz
###
##############################################################################
##############################################################################
* using log directory 'C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck'
* using R version 3.4.1 (2017-06-30)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'LEA/DESCRIPTION' ... OK
* this is package 'LEA' version '1.8.1'
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking whether package 'LEA' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* loading checks for arch 'i386'
** checking whether the package can be loaded ... OK
** checking whether the package can be loaded with stated dependencies ... OK
** checking whether the package can be unloaded cleanly ... OK
** checking whether the namespace can be loaded with stated dependencies ... OK
** checking whether the namespace can be unloaded cleanly ... OK
** checking loading without being on the library search path ... OK
* loading checks for arch 'x64'
** checking whether the package can be loaded ... OK
** checking whether the package can be loaded with stated dependencies ... OK
** checking whether the package can be unloaded cleanly ... OK
** checking whether the namespace can be loaded with stated dependencies ... OK
** checking whether the namespace can be unloaded cleanly ... OK
** checking loading without being on the library search path ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of 'data' directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking compiled code ... NOTE
Note: information on .o files for i386 is not available
Note: information on .o files for x64 is not available
File 'C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.buildbin-libdir/LEA/libs/i386/LEA.dll':
Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor the system RNG.
The detected symbols are linked into the code but might come from
libraries and not actually be called.
See 'Writing portable packages' in the 'Writing R Extensions' manual.
* checking installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... ERROR
Running examples in 'LEA-Ex.R' failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: snmf
> ### Title: Estimates individual ancestry coefficients and ancestral allele
> ### frequencies.
> ### Aliases: snmf plot,snmfProject-method cross.entropy,snmfProject-method
> ### load.snmfProject load.snmfProject,character-method remove.snmfProject
> ### remove.snmfProject,character-method import.snmfProject
> ### import.snmfProject,character-method export.snmfProject
> ### export.snmfProject,character-method combine.snmfProject
> ### combine.snmfProject,character,character-method
> ### show,snmfProject-method show,snmfClass-method
> ### summary,snmfProject-method Q,snmfProject-method G,snmfProject-method
> ### Keywords: snmf tutorial
>
> ### ** Examples
>
> ### Example of analyses using snmf ###
>
> # creation of the genotype file, genotypes.geno.
> # It contains 400 SNPs for 50 individuals.
> data("tutorial")
> write.geno(tutorial.R, "genotypes.geno")
[1] "genotypes.geno"
>
> ################
> # runs of snmf #
> ################
>
> # main options, K: (the number of ancestral populations),
> # entropy: calculate the cross-entropy criterion,
> # CPU: the number of CPUs.
>
> # Runs with K between 1 and 5 with cross-entropy and 2 repetitions.
> project = NULL
> project = snmf("genotypes.geno", K=1:10, entropy = TRUE, repetitions = 10,
+ project = "new")
The project is saved into :
genotypes.snmfProject
To load the project, use:
project = load.snmfProject("genotypes.snmfProject")
To remove the project, use:
remove.snmfProject("genotypes.snmfProject")
[1] 570175512
[1] "*************************************"
[1] "* create.dataset *"
[1] "*************************************"
summary of the options:
-n (number of individuals) 50
-L (number of loci) 400
-s (seed random init) 570175512
-r (percentage of masked data) 0.05
-x (genotype file in .geno format) C:\Users\biocbuild\bbs-3.5-bioc\meat\LEA.Rcheck\examples_i386\genotypes.geno
-o (output file in .geno format) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/masked/genotypes_I.geno
Write genotype file with masked data, C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/masked/genotypes_I.geno: OK.
[1] "*************************************"
[1] "* sNMF K = 1 repetition 1 *"
[1] "*************************************"
summary of the options:
-n (number of individuals) 50
-L (number of loci) 400
-K (number of ancestral pops) 1
-x (input file) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/masked/genotypes_I.geno
-q (individual admixture file) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K1/run1/genotypes_r1.1.Q
-g (ancestral frequencies file) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K1/run1/genotypes_r1.1.G
-i (number max of iterations) 200
-a (regularization parameter) 10
-s (seed random init) 570175512
-e (tolerance error) 1E-05
-p (number of processes) 1
- diploid
Read genotype file C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/masked/genotypes_I.geno: OK.
Main algorithm:
Least-square error: 6705.960082
Write individual ancestry coefficient file C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K1/run1/genotypes_r1.1.Q: OK.
Write ancestral allele frequency coefficient file C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K1/run1/genotypes_r1.1.G: OK.
[1] "*************************************"
[1] "* cross-entropy estimation *"
[1] "*************************************"
summary of the options:
-n (number of individuals) 50
-L (number of loci) 400
-K (number of ancestral pops) 1
-x (genotype file) C:\Users\biocbuild\bbs-3.5-bioc\meat\LEA.Rcheck\examples_i386\genotypes.geno
-q (individual admixture) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K1/run1/genotypes_r1.1.Q
-g (ancestral frequencies) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K1/run1/genotypes_r1.1.G
-i (with masked genotypes) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/masked/genotypes_I.geno
- diploid
Cross-Entropy (all data): 0.57967
Cross-Entropy (masked data): 0.591125
The project is saved into :
genotypes.snmfProject
To load the project, use:
project = load.snmfProject("genotypes.snmfProject")
To remove the project, use:
remove.snmfProject("genotypes.snmfProject")
[1] "*************************************"
[1] "* sNMF K = 2 repetition 1 *"
[1] "*************************************"
summary of the options:
-n (number of individuals) 50
-L (number of loci) 400
-K (number of ancestral pops) 2
-x (input file) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/masked/genotypes_I.geno
-q (individual admixture file) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K2/run1/genotypes_r1.2.Q
-g (ancestral frequencies file) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K2/run1/genotypes_r1.2.G
-i (number max of iterations) 200
-a (regularization parameter) 10
-s (seed random init) 570175512
-e (tolerance error) 1E-05
-p (number of processes) 1
- diploid
Read genotype file C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/masked/genotypes_I.geno: OK.
Main algorithm:
[ ]
[=========================]
Number of iterations: 68
Least-square error: 6148.892545
Write individual ancestry coefficient file C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K2/run1/genotypes_r1.2.Q: OK.
Write ancestral allele frequency coefficient file C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K2/run1/genotypes_r1.2.G: OK.
[1] "*************************************"
[1] "* cross-entropy estimation *"
[1] "*************************************"
summary of the options:
-n (number of individuals) 50
-L (number of loci) 400
-K (number of ancestral pops) 2
-x (genotype file) C:\Users\biocbuild\bbs-3.5-bioc\meat\LEA.Rcheck\examples_i386\genotypes.geno
-q (individual admixture) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K2/run1/genotypes_r1.2.Q
-g (ancestral frequencies) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K2/run1/genotypes_r1.2.G
-i (with masked genotypes) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/masked/genotypes_I.geno
- diploid
Cross-Entropy (all data): 0.522437
Cross-Entropy (masked data): 0.54456
The project is saved into :
genotypes.snmfProject
To load the project, use:
project = load.snmfProject("genotypes.snmfProject")
To remove the project, use:
remove.snmfProject("genotypes.snmfProject")
[1] "*************************************"
[1] "* sNMF K = 3 repetition 1 *"
[1] "*************************************"
summary of the options:
-n (number of individuals) 50
-L (number of loci) 400
-K (number of ancestral pops) 3
-x (input file) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/masked/genotypes_I.geno
-q (individual admixture file) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K3/run1/genotypes_r1.3.Q
-g (ancestral frequencies file) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K3/run1/genotypes_r1.3.G
-i (number max of iterations) 200
-a (regularization parameter) 10
-s (seed random init) 570175512
-e (tolerance error) 1E-05
-p (number of processes) 1
- diploid
Read genotype file C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/masked/genotypes_I.geno: OK.
Main algorithm:
[ ]
[================]
Number of iterations: 44
Least-square error: 5721.178495
Write individual ancestry coefficient file C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K3/run1/genotypes_r1.3.Q: OK.
Write ancestral allele frequency coefficient file C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K3/run1/genotypes_r1.3.G: OK.
[1] "*************************************"
[1] "* cross-entropy estimation *"
[1] "*************************************"
summary of the options:
-n (number of individuals) 50
-L (number of loci) 400
-K (number of ancestral pops) 3
-x (genotype file) C:\Users\biocbuild\bbs-3.5-bioc\meat\LEA.Rcheck\examples_i386\genotypes.geno
-q (individual admixture) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K3/run1/genotypes_r1.3.Q
-g (ancestral frequencies) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K3/run1/genotypes_r1.3.G
-i (with masked genotypes) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/masked/genotypes_I.geno
- diploid
Cross-Entropy (all data): 0.480778
Cross-Entropy (masked data): 0.503908
The project is saved into :
genotypes.snmfProject
To load the project, use:
project = load.snmfProject("genotypes.snmfProject")
To remove the project, use:
remove.snmfProject("genotypes.snmfProject")
[1] "*************************************"
[1] "* sNMF K = 4 repetition 1 *"
[1] "*************************************"
summary of the options:
-n (number of individuals) 50
-L (number of loci) 400
-K (number of ancestral pops) 4
-x (input file) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/masked/genotypes_I.geno
-q (individual admixture file) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K4/run1/genotypes_r1.4.Q
-g (ancestral frequencies file) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K4/run1/genotypes_r1.4.G
-i (number max of iterations) 200
-a (regularization parameter) 10
-s (seed random init) 570175512
-e (tolerance error) 1E-05
-p (number of processes) 1
- diploid
Read genotype file C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/masked/genotypes_I.geno: OK.
Main algorithm:
[ ]
[=====================]
Number of iterations: 57
Least-square error: 5484.522921
Write individual ancestry coefficient file C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K4/run1/genotypes_r1.4.Q: OK.
Write ancestral allele frequency coefficient file C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K4/run1/genotypes_r1.4.G: OK.
[1] "*************************************"
[1] "* cross-entropy estimation *"
[1] "*************************************"
summary of the options:
-n (number of individuals) 50
-L (number of loci) 400
-K (number of ancestral pops) 4
-x (genotype file) C:\Users\biocbuild\bbs-3.5-bioc\meat\LEA.Rcheck\examples_i386\genotypes.geno
-q (individual admixture) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K4/run1/genotypes_r1.4.Q
-g (ancestral frequencies) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K4/run1/genotypes_r1.4.G
-i (with masked genotypes) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/masked/genotypes_I.geno
- diploid
Cross-Entropy (all data): 0.454338
Cross-Entropy (masked data): 0.506725
The project is saved into :
genotypes.snmfProject
To load the project, use:
project = load.snmfProject("genotypes.snmfProject")
To remove the project, use:
remove.snmfProject("genotypes.snmfProject")
[1] "*************************************"
[1] "* sNMF K = 5 repetition 1 *"
[1] "*************************************"
summary of the options:
-n (number of individuals) 50
-L (number of loci) 400
-K (number of ancestral pops) 5
-x (input file) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/masked/genotypes_I.geno
-q (individual admixture file) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K5/run1/genotypes_r1.5.Q
-g (ancestral frequencies file) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K5/run1/genotypes_r1.5.G
-i (number max of iterations) 200
-a (regularization parameter) 10
-s (seed random init) 570175512
-e (tolerance error) 1E-05
-p (number of processes) 1
- diploid
Read genotype file C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/masked/genotypes_I.geno: OK.
Main algorithm:
[ ]
[=====================]
Number of iterations: 57
Least-square error: 5268.407003
Write individual ancestry coefficient file C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K5/run1/genotypes_r1.5.Q: OK.
Write ancestral allele frequency coefficient file C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K5/run1/genotypes_r1.5.G: OK.
[1] "*************************************"
[1] "* cross-entropy estimation *"
[1] "*************************************"
summary of the options:
-n (number of individuals) 50
-L (number of loci) 400
-K (number of ancestral pops) 5
-x (genotype file) C:\Users\biocbuild\bbs-3.5-bioc\meat\LEA.Rcheck\examples_i386\genotypes.geno
-q (individual admixture) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K5/run1/genotypes_r1.5.Q
-g (ancestral frequencies) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K5/run1/genotypes_r1.5.G
-i (with masked genotypes) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/masked/genotypes_I.geno
- diploid
Cross-Entropy (all data): 0.434343
Cross-Entropy (masked data): 0.527437
The project is saved into :
genotypes.snmfProject
To load the project, use:
project = load.snmfProject("genotypes.snmfProject")
To remove the project, use:
remove.snmfProject("genotypes.snmfProject")
[1] "*************************************"
[1] "* sNMF K = 6 repetition 1 *"
[1] "*************************************"
summary of the options:
-n (number of individuals) 50
-L (number of loci) 400
-K (number of ancestral pops) 6
-x (input file) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/masked/genotypes_I.geno
-q (individual admixture file) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K6/run1/genotypes_r1.6.Q
-g (ancestral frequencies file) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K6/run1/genotypes_r1.6.G
-i (number max of iterations) 200
-a (regularization parameter) 10
-s (seed random init) 570175512
-e (tolerance error) 1E-05
-p (number of processes) 1
- diploid
Read genotype file C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/masked/genotypes_I.geno: OK.
Main algorithm:
[ ]
[=============================]
Number of iterations: 78
Least-square error: 5109.963742
Write individual ancestry coefficient file C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K6/run1/genotypes_r1.6.Q: OK.
Write ancestral allele frequency coefficient file C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K6/run1/genotypes_r1.6.G: OK.
[1] "*************************************"
[1] "* cross-entropy estimation *"
[1] "*************************************"
summary of the options:
-n (number of individuals) 50
-L (number of loci) 400
-K (number of ancestral pops) 6
-x (genotype file) C:\Users\biocbuild\bbs-3.5-bioc\meat\LEA.Rcheck\examples_i386\genotypes.geno
-q (individual admixture) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K6/run1/genotypes_r1.6.Q
-g (ancestral frequencies) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K6/run1/genotypes_r1.6.G
-i (with masked genotypes) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/masked/genotypes_I.geno
- diploid
Cross-Entropy (all data): 0.421739
Cross-Entropy (masked data): 0.586105
The project is saved into :
genotypes.snmfProject
To load the project, use:
project = load.snmfProject("genotypes.snmfProject")
To remove the project, use:
remove.snmfProject("genotypes.snmfProject")
[1] "*************************************"
[1] "* sNMF K = 7 repetition 1 *"
[1] "*************************************"
summary of the options:
-n (number of individuals) 50
-L (number of loci) 400
-K (number of ancestral pops) 7
-x (input file) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/masked/genotypes_I.geno
-q (individual admixture file) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K7/run1/genotypes_r1.7.Q
-g (ancestral frequencies file) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K7/run1/genotypes_r1.7.G
-i (number max of iterations) 200
-a (regularization parameter) 10
-s (seed random init) 570175512
-e (tolerance error) 1E-05
-p (number of processes) 1
- diploid
Read genotype file C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/masked/genotypes_I.geno: OK.
Main algorithm:
[ ]
[===================================================]
Number of iterations: 137
Least-square error: 4970.256787
Write individual ancestry coefficient file C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K7/run1/genotypes_r1.7.Q: OK.
Write ancestral allele frequency coefficient file C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K7/run1/genotypes_r1.7.G: OK.
[1] "*************************************"
[1] "* cross-entropy estimation *"
[1] "*************************************"
summary of the options:
-n (number of individuals) 50
-L (number of loci) 400
-K (number of ancestral pops) 7
-x (genotype file) C:\Users\biocbuild\bbs-3.5-bioc\meat\LEA.Rcheck\examples_i386\genotypes.geno
-q (individual admixture) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K7/run1/genotypes_r1.7.Q
-g (ancestral frequencies) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K7/run1/genotypes_r1.7.G
-i (with masked genotypes) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/masked/genotypes_I.geno
- diploid
Cross-Entropy (all data): 0.407338
Cross-Entropy (masked data): 0.547976
The project is saved into :
genotypes.snmfProject
To load the project, use:
project = load.snmfProject("genotypes.snmfProject")
To remove the project, use:
remove.snmfProject("genotypes.snmfProject")
[1] "*************************************"
[1] "* sNMF K = 8 repetition 1 *"
[1] "*************************************"
summary of the options:
-n (number of individuals) 50
-L (number of loci) 400
-K (number of ancestral pops) 8
-x (input file) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/masked/genotypes_I.geno
-q (individual admixture file) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K8/run1/genotypes_r1.8.Q
-g (ancestral frequencies file) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K8/run1/genotypes_r1.8.G
-i (number max of iterations) 200
-a (regularization parameter) 10
-s (seed random init) 570175512
-e (tolerance error) 1E-05
-p (number of processes) 1
- diploid
Read genotype file C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/masked/genotypes_I.geno: OK.
Main algorithm:
[ ]
[=============]
Number of iterations: 34
Least-square error: 4843.497280
Write individual ancestry coefficient file C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K8/run1/genotypes_r1.8.Q: OK.
Write ancestral allele frequency coefficient file C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K8/run1/genotypes_r1.8.G: OK.
[1] "*************************************"
[1] "* cross-entropy estimation *"
[1] "*************************************"
summary of the options:
-n (number of individuals) 50
-L (number of loci) 400
-K (number of ancestral pops) 8
-x (genotype file) C:\Users\biocbuild\bbs-3.5-bioc\meat\LEA.Rcheck\examples_i386\genotypes.geno
-q (individual admixture) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K8/run1/genotypes_r1.8.Q
-g (ancestral frequencies) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K8/run1/genotypes_r1.8.G
-i (with masked genotypes) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/masked/genotypes_I.geno
- diploid
Cross-Entropy (all data): 0.394053
Cross-Entropy (masked data): 0.613664
The project is saved into :
genotypes.snmfProject
To load the project, use:
project = load.snmfProject("genotypes.snmfProject")
To remove the project, use:
remove.snmfProject("genotypes.snmfProject")
[1] "*************************************"
[1] "* sNMF K = 9 repetition 1 *"
[1] "*************************************"
summary of the options:
-n (number of individuals) 50
-L (number of loci) 400
-K (number of ancestral pops) 9
-x (input file) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/masked/genotypes_I.geno
-q (individual admixture file) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K9/run1/genotypes_r1.9.Q
-g (ancestral frequencies file) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K9/run1/genotypes_r1.9.G
-i (number max of iterations) 200
-a (regularization parameter) 10
-s (seed random init) 570175512
-e (tolerance error) 1E-05
-p (number of processes) 1
- diploid
Read genotype file C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/masked/genotypes_I.geno: OK.
Main algorithm:
[ ]
[===============================]
Number of iterations: 83
Least-square error: 4690.388520
Write individual ancestry coefficient file C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K9/run1/genotypes_r1.9.Q: OK.
Write ancestral allele frequency coefficient file C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K9/run1/genotypes_r1.9.G: OK.
[1] "*************************************"
[1] "* cross-entropy estimation *"
[1] "*************************************"
summary of the options:
-n (number of individuals) 50
-L (number of loci) 400
-K (number of ancestral pops) 9
-x (genotype file) C:\Users\biocbuild\bbs-3.5-bioc\meat\LEA.Rcheck\examples_i386\genotypes.geno
-q (individual admixture) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K9/run1/genotypes_r1.9.Q
-g (ancestral frequencies) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K9/run1/genotypes_r1.9.G
-i (with masked genotypes) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/masked/genotypes_I.geno
- diploid
Cross-Entropy (all data): 0.380741
Cross-Entropy (masked data): 0.63184
The project is saved into :
genotypes.snmfProject
To load the project, use:
project = load.snmfProject("genotypes.snmfProject")
To remove the project, use:
remove.snmfProject("genotypes.snmfProject")
[1] "*************************************"
[1] "* sNMF K = 10 repetition 1 *"
[1] "*************************************"
summary of the options:
-n (number of individuals) 50
-L (number of loci) 400
-K (number of ancestral pops) 10
-x (input file) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/masked/genotypes_I.geno
-q (individual admixture file) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K10/run1/genotypes_r1.10.Q
-g (ancestral frequencies file) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K10/run1/genotypes_r1.10.G
-i (number max of iterations) 200
-a (regularization parameter) 10
-s (seed random init) 570175512
-e (tolerance error) 1E-05
-p (number of processes) 1
- diploid
Read genotype file C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/masked/genotypes_I.geno: OK.
Main algorithm:
[ ]
[========================================]
Number of iterations: 107
Least-square error: 4537.572076
Write individual ancestry coefficient file C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K10/run1/genotypes_r1.10.Q: OK.
Write ancestral allele frequency coefficient file C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K10/run1/genotypes_r1.10.G: OK.
[1] "*************************************"
[1] "* cross-entropy estimation *"
[1] "*************************************"
summary of the options:
-n (number of individuals) 50
-L (number of loci) 400
-K (number of ancestral pops) 10
-x (genotype file) C:\Users\biocbuild\bbs-3.5-bioc\meat\LEA.Rcheck\examples_i386\genotypes.geno
-q (individual admixture) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K10/run1/genotypes_r1.10.Q
-g (ancestral frequencies) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K10/run1/genotypes_r1.10.G
-i (with masked genotypes) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/masked/genotypes_I.geno
- diploid
Cross-Entropy (all data): 0.368318
Cross-Entropy (masked data): 0.624159
The project is saved into :
genotypes.snmfProject
To load the project, use:
project = load.snmfProject("genotypes.snmfProject")
To remove the project, use:
remove.snmfProject("genotypes.snmfProject")
[1] 1239947635
[1] "*************************************"
[1] "* create.dataset *"
[1] "*************************************"
summary of the options:
-n (number of individuals) 50
-L (number of loci) 400
-s (seed random init) 1239947635
-r (percentage of masked data) 0.05
-x (genotype file in .geno format) C:\Users\biocbuild\bbs-3.5-bioc\meat\LEA.Rcheck\examples_i386\genotypes.geno
-o (output file in .geno format) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/masked/genotypes_I.geno
Write genotype file with masked data, C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/masked/genotypes_I.geno: OK.
[1] "*************************************"
[1] "* sNMF K = 1 repetition 2 *"
[1] "*************************************"
summary of the options:
-n (number of individuals) 50
-L (number of loci) 400
-K (number of ancestral pops) 1
-x (input file) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/masked/genotypes_I.geno
-q (individual admixture file) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K1/run2/genotypes_r2.1.Q
-g (ancestral frequencies file) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K1/run2/genotypes_r2.1.G
-i (number max of iterations) 200
-a (regularization parameter) 10
-s (seed random init) 1239947635
-e (tolerance error) 1E-05
-p (number of processes) 1
- diploid
Read genotype file C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/masked/genotypes_I.geno: OK.
Main algorithm:
Least-square error: 6669.400085
Write individual ancestry coefficient file C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K1/run2/genotypes_r2.1.Q: OK.
Write ancestral allele frequency coefficient file C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K1/run2/genotypes_r2.1.G: OK.
[1] "*************************************"
[1] "* cross-entropy estimation *"
[1] "*************************************"
summary of the options:
-n (number of individuals) 50
-L (number of loci) 400
-K (number of ancestral pops) 1
-x (genotype file) C:\Users\biocbuild\bbs-3.5-bioc\meat\LEA.Rcheck\examples_i386\genotypes.geno
-q (individual admixture) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K1/run2/genotypes_r2.1.Q
-g (ancestral frequencies) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K1/run2/genotypes_r2.1.G
-i (with masked genotypes) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/masked/genotypes_I.geno
- diploid
Cross-Entropy (all data): 0.577323
Cross-Entropy (masked data): 0.665395
The project is saved into :
genotypes.snmfProject
To load the project, use:
project = load.snmfProject("genotypes.snmfProject")
To remove the project, use:
remove.snmfProject("genotypes.snmfProject")
[1] "*************************************"
[1] "* sNMF K = 2 repetition 2 *"
[1] "*************************************"
summary of the options:
-n (number of individuals) 50
-L (number of loci) 400
-K (number of ancestral pops) 2
-x (input file) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/masked/genotypes_I.geno
-q (individual admixture file) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K2/run2/genotypes_r2.2.Q
-g (ancestral frequencies file) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K2/run2/genotypes_r2.2.G
-i (number max of iterations) 200
-a (regularization parameter) 10
-s (seed random init) 1239947635
-e (tolerance error) 1E-05
-p (number of processes) 1
- diploid
Read genotype file C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/masked/genotypes_I.geno: OK.
Main algorithm:
[ ]
[===========]
Number of iterations: 29
Least-square error: 6129.628211
Write individual ancestry coefficient file C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K2/run2/genotypes_r2.2.Q: OK.
Write ancestral allele frequency coefficient file C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K2/run2/genotypes_r2.2.G: OK.
[1] "*************************************"
[1] "* cross-entropy estimation *"
[1] "*************************************"
summary of the options:
-n (number of individuals) 50
-L (number of loci) 400
-K (number of ancestral pops) 2
-x (genotype file) C:\Users\biocbuild\bbs-3.5-bioc\meat\LEA.Rcheck\examples_i386\genotypes.geno
-q (individual admixture) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K2/run2/genotypes_r2.2.Q
-g (ancestral frequencies) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K2/run2/genotypes_r2.2.G
-i (with masked genotypes) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/masked/genotypes_I.geno
- diploid
Cross-Entropy (all data): 0.519076
Cross-Entropy (masked data): 0.645858
The project is saved into :
genotypes.snmfProject
To load the project, use:
project = load.snmfProject("genotypes.snmfProject")
To remove the project, use:
remove.snmfProject("genotypes.snmfProject")
[1] "*************************************"
[1] "* sNMF K = 3 repetition 2 *"
[1] "*************************************"
summary of the options:
-n (number of individuals) 50
-L (number of loci) 400
-K (number of ancestral pops) 3
-x (input file) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/masked/genotypes_I.geno
-q (individual admixture file) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K3/run2/genotypes_r2.3.Q
-g (ancestral frequencies file) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K3/run2/genotypes_r2.3.G
-i (number max of iterations) 200
-a (regularization parameter) 10
-s (seed random init) 1239947635
-e (tolerance error) 1E-05
-p (number of processes) 1
- diploid
Read genotype file C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/masked/genotypes_I.geno: OK.
Main algorithm:
[ ]
[=====================]
Number of iterations: 57
Least-square error: 5729.993018
Write individual ancestry coefficient file C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K3/run2/genotypes_r2.3.Q: OK.
Write ancestral allele frequency coefficient file C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K3/run2/genotypes_r2.3.G: OK.
[1] "*************************************"
[1] "* cross-entropy estimation *"
[1] "*************************************"
summary of the options:
-n (number of individuals) 50
-L (number of loci) 400
-K (number of ancestral pops) 3
-x (genotype file) C:\Users\biocbuild\bbs-3.5-bioc\meat\LEA.Rcheck\examples_i386\genotypes.geno
-q (individual admixture) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K3/run2/genotypes_r2.3.Q
-g (ancestral frequencies) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K3/run2/genotypes_r2.3.G
-i (with masked genotypes) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/masked/genotypes_I.geno
- diploid
Cross-Entropy (all data): 0.478577
Cross-Entropy (masked data): 0.613406
The project is saved into :
genotypes.snmfProject
To load the project, use:
project = load.snmfProject("genotypes.snmfProject")
To remove the project, use:
remove.snmfProject("genotypes.snmfProject")
[1] "*************************************"
[1] "* sNMF K = 4 repetition 2 *"
[1] "*************************************"
summary of the options:
-n (number of individuals) 50
-L (number of loci) 400
-K (number of ancestral pops) 4
-x (input file) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/masked/genotypes_I.geno
-q (individual admixture file) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K4/run2/genotypes_r2.4.Q
-g (ancestral frequencies file) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K4/run2/genotypes_r2.4.G
-i (number max of iterations) 200
-a (regularization parameter) 10
-s (seed random init) 1239947635
-e (tolerance error) 1E-05
-p (number of processes) 1
- diploid
Read genotype file C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/masked/genotypes_I.geno: OK.
Main algorithm:
[ ]
[=================]
Number of iterations: 46
Least-square error: 5472.444161
Write individual ancestry coefficient file C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K4/run2/genotypes_r2.4.Q: OK.
Write ancestral allele frequency coefficient file C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K4/run2/genotypes_r2.4.G: OK.
[1] "*************************************"
[1] "* cross-entropy estimation *"
[1] "*************************************"
summary of the options:
-n (number of individuals) 50
-L (number of loci) 400
-K (number of ancestral pops) 4
-x (genotype file) C:\Users\biocbuild\bbs-3.5-bioc\meat\LEA.Rcheck\examples_i386\genotypes.geno
-q (individual admixture) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K4/run2/genotypes_r2.4.Q
-g (ancestral frequencies) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K4/run2/genotypes_r2.4.G
-i (with masked genotypes) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/masked/genotypes_I.geno
- diploid
Cross-Entropy (all data): 0.45452
Cross-Entropy (masked data): 0.597298
The project is saved into :
genotypes.snmfProject
To load the project, use:
project = load.snmfProject("genotypes.snmfProject")
To remove the project, use:
remove.snmfProject("genotypes.snmfProject")
[1] "*************************************"
[1] "* sNMF K = 5 repetition 2 *"
[1] "*************************************"
summary of the options:
-n (number of individuals) 50
-L (number of loci) 400
-K (number of ancestral pops) 5
-x (input file) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/masked/genotypes_I.geno
-q (individual admixture file) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K5/run2/genotypes_r2.5.Q
-g (ancestral frequencies file) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K5/run2/genotypes_r2.5.G
-i (number max of iterations) 200
-a (regularization parameter) 10
-s (seed random init) 1239947635
-e (tolerance error) 1E-05
-p (number of processes) 1
- diploid
Read genotype file C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/masked/genotypes_I.geno: OK.
Main algorithm:
[ ]
[==============================================]
Number of iterations: 124
Least-square error: 5244.400286
Write individual ancestry coefficient file C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K5/run2/genotypes_r2.5.Q: OK.
Write ancestral allele frequency coefficient file C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K5/run2/genotypes_r2.5.G: OK.
[1] "*************************************"
[1] "* cross-entropy estimation *"
[1] "*************************************"
summary of the options:
-n (number of individuals) 50
-L (number of loci) 400
-K (number of ancestral pops) 5
-x (genotype file) C:\Users\biocbuild\bbs-3.5-bioc\meat\LEA.Rcheck\examples_i386\genotypes.geno
-q (individual admixture) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K5/run2/genotypes_r2.5.Q
-g (ancestral frequencies) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K5/run2/genotypes_r2.5.G
-i (with masked genotypes) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/masked/genotypes_I.geno
- diploid
Cross-Entropy (all data): 0.433098
Cross-Entropy (masked data): 0.61917
The project is saved into :
genotypes.snmfProject
To load the project, use:
project = load.snmfProject("genotypes.snmfProject")
To remove the project, use:
remove.snmfProject("genotypes.snmfProject")
[1] "*************************************"
[1] "* sNMF K = 6 repetition 2 *"
[1] "*************************************"
summary of the options:
-n (number of individuals) 50
-L (number of loci) 400
-K (number of ancestral pops) 6
-x (input file) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/masked/genotypes_I.geno
-q (individual admixture file) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K6/run2/genotypes_r2.6.Q
-g (ancestral frequencies file) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K6/run2/genotypes_r2.6.G
-i (number max of iterations) 200
-a (regularization parameter) 10
-s (seed random init) 1239947635
-e (tolerance error) 1E-05
-p (number of processes) 1
- diploid
Read genotype file C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/masked/genotypes_I.geno: OK.
Main algorithm:
[ ]
[============]
Number of iterations: 31
Least-square error: 5072.408333
Write individual ancestry coefficient file C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K6/run2/genotypes_r2.6.Q: OK.
Write ancestral allele frequency coefficient file C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K6/run2/genotypes_r2.6.G: OK.
[1] "*************************************"
[1] "* cross-entropy estimation *"
[1] "*************************************"
summary of the options:
-n (number of individuals) 50
-L (number of loci) 400
-K (number of ancestral pops) 6
-x (genotype file) C:\Users\biocbuild\bbs-3.5-bioc\meat\LEA.Rcheck\examples_i386\genotypes.geno
-q (individual admixture) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K6/run2/genotypes_r2.6.Q
-g (ancestral frequencies) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K6/run2/genotypes_r2.6.G
-i (with masked genotypes) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/masked/genotypes_I.geno
- diploid
Cross-Entropy (all data): 0.419443
Cross-Entropy (masked data): 0.645884
The project is saved into :
genotypes.snmfProject
To load the project, use:
project = load.snmfProject("genotypes.snmfProject")
To remove the project, use:
remove.snmfProject("genotypes.snmfProject")
[1] "*************************************"
[1] "* sNMF K = 7 repetition 2 *"
[1] "*************************************"
summary of the options:
-n (number of individuals) 50
-L (number of loci) 400
-K (number of ancestral pops) 7
-x (input file) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/masked/genotypes_I.geno
-q (individual admixture file) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K7/run2/genotypes_r2.7.Q
-g (ancestral frequencies file) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K7/run2/genotypes_r2.7.G
-i (number max of iterations) 200
-a (regularization parameter) 10
-s (seed random init) 1239947635
-e (tolerance error) 1E-05
-p (number of processes) 1
- diploid
Read genotype file C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/masked/genotypes_I.geno: OK.
Main algorithm:
[ ]
[===============]
Number of iterations: 39
Least-square error: 4950.927150
Write individual ancestry coefficient file C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K7/run2/genotypes_r2.7.Q: OK.
Write ancestral allele frequency coefficient file C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K7/run2/genotypes_r2.7.G: OK.
[1] "*************************************"
[1] "* cross-entropy estimation *"
[1] "*************************************"
summary of the options:
-n (number of individuals) 50
-L (number of loci) 400
-K (number of ancestral pops) 7
-x (genotype file) C:\Users\biocbuild\bbs-3.5-bioc\meat\LEA.Rcheck\examples_i386\genotypes.geno
-q (individual admixture) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K7/run2/genotypes_r2.7.Q
-g (ancestral frequencies) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K7/run2/genotypes_r2.7.G
-i (with masked genotypes) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/masked/genotypes_I.geno
- diploid
Cross-Entropy (all data): 0.406688
Cross-Entropy (masked data): 0.630021
The project is saved into :
genotypes.snmfProject
To load the project, use:
project = load.snmfProject("genotypes.snmfProject")
To remove the project, use:
remove.snmfProject("genotypes.snmfProject")
[1] "*************************************"
[1] "* sNMF K = 8 repetition 2 *"
[1] "*************************************"
summary of the options:
-n (number of individuals) 50
-L (number of loci) 400
-K (number of ancestral pops) 8
-x (input file) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/masked/genotypes_I.geno
-q (individual admixture file) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K8/run2/genotypes_r2.8.Q
-g (ancestral frequencies file) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K8/run2/genotypes_r2.8.G
-i (number max of iterations) 200
-a (regularization parameter) 10
-s (seed random init) 1239947635
-e (tolerance error) 1E-05
-p (number of processes) 1
- diploid
Read genotype file C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/masked/genotypes_I.geno: OK.
Main algorithm:
[ ]
[=================]
Number of iterations: 45
Least-square error: 4791.883286
Write individual ancestry coefficient file C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K8/run2/genotypes_r2.8.Q: OK.
Write ancestral allele frequency coefficient file C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K8/run2/genotypes_r2.8.G: OK.
[1] "*************************************"
[1] "* cross-entropy estimation *"
[1] "*************************************"
summary of the options:
-n (number of individuals) 50
-L (number of loci) 400
-K (number of ancestral pops) 8
-x (genotype file) C:\Users\biocbuild\bbs-3.5-bioc\meat\LEA.Rcheck\examples_i386\genotypes.geno
-q (individual admixture) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K8/run2/genotypes_r2.8.Q
-g (ancestral frequencies) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K8/run2/genotypes_r2.8.G
-i (with masked genotypes) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/masked/genotypes_I.geno
- diploid
Cross-Entropy (all data): 0.39229
Cross-Entropy (masked data): 0.656944
The project is saved into :
genotypes.snmfProject
To load the project, use:
project = load.snmfProject("genotypes.snmfProject")
To remove the project, use:
remove.snmfProject("genotypes.snmfProject")
[1] "*************************************"
[1] "* sNMF K = 9 repetition 2 *"
[1] "*************************************"
summary of the options:
-n (number of individuals) 50
-L (number of loci) 400
-K (number of ancestral pops) 9
-x (input file) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/masked/genotypes_I.geno
-q (individual admixture file) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K9/run2/genotypes_r2.9.Q
-g (ancestral frequencies file) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K9/run2/genotypes_r2.9.G
-i (number max of iterations) 200
-a (regularization parameter) 10
-s (seed random init) 1239947635
-e (tolerance error) 1E-05
-p (number of processes) 1
- diploid
Read genotype file C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/masked/genotypes_I.geno: OK.
Main algorithm:
[ ]
[=======================================]
Number of iterations: 104
Least-square error: 4651.243958
Write individual ancestry coefficient file C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K9/run2/genotypes_r2.9.Q: OK.
Write ancestral allele frequency coefficient file C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K9/run2/genotypes_r2.9.G: OK.
[1] "*************************************"
[1] "* cross-entropy estimation *"
[1] "*************************************"
summary of the options:
-n (number of individuals) 50
-L (number of loci) 400
-K (number of ancestral pops) 9
-x (genotype file) C:\Users\biocbuild\bbs-3.5-bioc\meat\LEA.Rcheck\examples_i386\genotypes.geno
-q (individual admixture) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K9/run2/genotypes_r2.9.Q
-g (ancestral frequencies) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K9/run2/genotypes_r2.9.G
-i (with masked genotypes) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/masked/genotypes_I.geno
- diploid
Cross-Entropy (all data): 0.381792
Cross-Entropy (masked data): 0.686569
The project is saved into :
genotypes.snmfProject
To load the project, use:
project = load.snmfProject("genotypes.snmfProject")
To remove the project, use:
remove.snmfProject("genotypes.snmfProject")
[1] "*************************************"
[1] "* sNMF K = 10 repetition 2 *"
[1] "*************************************"
summary of the options:
-n (number of individuals) 50
-L (number of loci) 400
-K (number of ancestral pops) 10
-x (input file) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/masked/genotypes_I.geno
-q (individual admixture file) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K10/run2/genotypes_r2.10.Q
-g (ancestral frequencies file) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K10/run2/genotypes_r2.10.G
-i (number max of iterations) 200
-a (regularization parameter) 10
-s (seed random init) 1239947635
-e (tolerance error) 1E-05
-p (number of processes) 1
- diploid
Read genotype file C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/masked/genotypes_I.geno: OK.
Main algorithm:
[ ]
[==================]
Number of iterations: 49
Least-square error: 4528.756561
Write individual ancestry coefficient file C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K10/run2/genotypes_r2.10.Q: OK.
Write ancestral allele frequency coefficient file C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K10/run2/genotypes_r2.10.G: OK.
[1] "*************************************"
[1] "* cross-entropy estimation *"
[1] "*************************************"
summary of the options:
-n (number of individuals) 50
-L (number of loci) 400
-K (number of ancestral pops) 10
-x (genotype file) C:\Users\biocbuild\bbs-3.5-bioc\meat\LEA.Rcheck\examples_i386\genotypes.geno
-q (individual admixture) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K10/run2/genotypes_r2.10.Q
-g (ancestral frequencies) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K10/run2/genotypes_r2.10.G
-i (with masked genotypes) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/masked/genotypes_I.geno
- diploid
Cross-Entropy (all data): 0.37042
Cross-Entropy (masked data): 0.668726
The project is saved into :
genotypes.snmfProject
To load the project, use:
project = load.snmfProject("genotypes.snmfProject")
To remove the project, use:
remove.snmfProject("genotypes.snmfProject")
[1] 1663831666
[1] "*************************************"
[1] "* create.dataset *"
[1] "*************************************"
summary of the options:
-n (number of individuals) 50
-L (number of loci) 400
-s (seed random init) 1663831666
-r (percentage of masked data) 0.05
-x (genotype file in .geno format) C:\Users\biocbuild\bbs-3.5-bioc\meat\LEA.Rcheck\examples_i386\genotypes.geno
-o (output file in .geno format) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/masked/genotypes_I.geno
Write genotype file with masked data, C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/masked/genotypes_I.geno: OK.
[1] "*************************************"
[1] "* sNMF K = 1 repetition 3 *"
[1] "*************************************"
summary of the options:
-n (number of individuals) 50
-L (number of loci) 400
-K (number of ancestral pops) 1
-x (input file) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/masked/genotypes_I.geno
-q (individual admixture file) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K1/run3/genotypes_r3.1.Q
-g (ancestral frequencies file) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K1/run3/genotypes_r3.1.G
-i (number max of iterations) 200
-a (regularization parameter) 10
-s (seed random init) 1663831666
-e (tolerance error) 1E-05
-p (number of processes) 1
- diploid
Read genotype file C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/masked/genotypes_I.geno: OK.
Main algorithm:
Least-square error: 6702.240081
Write individual ancestry coefficient file C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K1/run3/genotypes_r3.1.Q: OK.
Write ancestral allele frequency coefficient file C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K1/run3/genotypes_r3.1.G: OK.
[1] "*************************************"
[1] "* cross-entropy estimation *"
[1] "*************************************"
summary of the options:
-n (number of individuals) 50
-L (number of loci) 400
-K (number of ancestral pops) 1
-x (genotype file) C:\Users\biocbuild\bbs-3.5-bioc\meat\LEA.Rcheck\examples_i386\genotypes.geno
-q (individual admixture) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K1/run3/genotypes_r3.1.Q
-g (ancestral frequencies) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K1/run3/genotypes_r3.1.G
-i (with masked genotypes) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/masked/genotypes_I.geno
- diploid
Cross-Entropy (all data): 0.579022
Cross-Entropy (masked data): 0.598327
The project is saved into :
genotypes.snmfProject
To load the project, use:
project = load.snmfProject("genotypes.snmfProject")
To remove the project, use:
remove.snmfProject("genotypes.snmfProject")
[1] "*************************************"
[1] "* sNMF K = 2 repetition 3 *"
[1] "*************************************"
summary of the options:
-n (number of individuals) 50
-L (number of loci) 400
-K (number of ancestral pops) 2
-x (input file) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/masked/genotypes_I.geno
-q (individual admixture file) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K2/run3/genotypes_r3.2.Q
-g (ancestral frequencies file) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K2/run3/genotypes_r3.2.G
-i (number max of iterations) 200
-a (regularization parameter) 10
-s (seed random init) 1663831666
-e (tolerance error) 1E-05
-p (number of processes) 1
- diploid
Read genotype file C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/masked/genotypes_I.geno: OK.
Main algorithm:
[ ]
[=====================]
Number of iterations: 57
Least-square error: 6162.763418
Write individual ancestry coefficient file C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K2/run3/genotypes_r3.2.Q: OK.
Write ancestral allele frequency coefficient file C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K2/run3/genotypes_r3.2.G: OK.
[1] "*************************************"
[1] "* cross-entropy estimation *"
[1] "*************************************"
summary of the options:
-n (number of individuals) 50
-L (number of loci) 400
-K (number of ancestral pops) 2
-x (genotype file) C:\Users\biocbuild\bbs-3.5-bioc\meat\LEA.Rcheck\examples_i386\genotypes.geno
-q (individual admixture) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K2/run3/genotypes_r3.2.Q
-g (ancestral frequencies) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K2/run3/genotypes_r3.2.G
-i (with masked genotypes) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/masked/genotypes_I.geno
- diploid
Cross-Entropy (all data): 0.519857
Cross-Entropy (masked data): 0.571468
The project is saved into :
genotypes.snmfProject
To load the project, use:
project = load.snmfProject("genotypes.snmfProject")
To remove the project, use:
remove.snmfProject("genotypes.snmfProject")
[1] "*************************************"
[1] "* sNMF K = 3 repetition 3 *"
[1] "*************************************"
summary of the options:
-n (number of individuals) 50
-L (number of loci) 400
-K (number of ancestral pops) 3
-x (input file) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/masked/genotypes_I.geno
-q (individual admixture file) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K3/run3/genotypes_r3.3.Q
-g (ancestral frequencies file) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K3/run3/genotypes_r3.3.G
-i (number max of iterations) 200
-a (regularization parameter) 10
-s (seed random init) 1663831666
-e (tolerance error) 1E-05
-p (number of processes) 1
- diploid
Read genotype file C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/masked/genotypes_I.geno: OK.
Main algorithm:
[ ]
[======================]
Number of iterations: 58
Least-square error: 5716.426733
Write individual ancestry coefficient file C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K3/run3/genotypes_r3.3.Q: OK.
Write ancestral allele frequency coefficient file C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K3/run3/genotypes_r3.3.G: OK.
[1] "*************************************"
[1] "* cross-entropy estimation *"
[1] "*************************************"
summary of the options:
-n (number of individuals) 50
-L (number of loci) 400
-K (number of ancestral pops) 3
-x (genotype file) C:\Users\biocbuild\bbs-3.5-bioc\meat\LEA.Rcheck\examples_i386\genotypes.geno
-q (individual admixture) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K3/run3/genotypes_r3.3.Q
-g (ancestral frequencies) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K3/run3/genotypes_r3.3.G
-i (with masked genotypes) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/masked/genotypes_I.geno
- diploid
Cross-Entropy (all data): 0.479154
Cross-Entropy (masked data): 0.564943
The project is saved into :
genotypes.snmfProject
To load the project, use:
project = load.snmfProject("genotypes.snmfProject")
To remove the project, use:
remove.snmfProject("genotypes.snmfProject")
[1] "*************************************"
[1] "* sNMF K = 4 repetition 3 *"
[1] "*************************************"
summary of the options:
-n (number of individuals) 50
-L (number of loci) 400
-K (number of ancestral pops) 4
-x (input file) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/masked/genotypes_I.geno
-q (individual admixture file) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K4/run3/genotypes_r3.4.Q
-g (ancestral frequencies file) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K4/run3/genotypes_r3.4.G
-i (number max of iterations) 200
-a (regularization parameter) 10
-s (seed random init) 1663831666
-e (tolerance error) 1E-05
-p (number of processes) 1
- diploid
Read genotype file C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/masked/genotypes_I.geno: OK.
Main algorithm:
[ ]
[========================]
Number of iterations: 64
Least-square error: 5474.715036
Write individual ancestry coefficient file C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K4/run3/genotypes_r3.4.Q: OK.
Write ancestral allele frequency coefficient file C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K4/run3/genotypes_r3.4.G: OK.
[1] "*************************************"
[1] "* cross-entropy estimation *"
[1] "*************************************"
summary of the options:
-n (number of individuals) 50
-L (number of loci) 400
-K (number of ancestral pops) 4
-x (genotype file) C:\Users\biocbuild\bbs-3.5-bioc\meat\LEA.Rcheck\examples_i386\genotypes.geno
-q (individual admixture) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K4/run3/genotypes_r3.4.Q
-g (ancestral frequencies) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K4/run3/genotypes_r3.4.G
-i (with masked genotypes) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/masked/genotypes_I.geno
- diploid
Cross-Entropy (all data): 0.452678
Cross-Entropy (masked data): 0.570817
The project is saved into :
genotypes.snmfProject
To load the project, use:
project = load.snmfProject("genotypes.snmfProject")
To remove the project, use:
remove.snmfProject("genotypes.snmfProject")
[1] "*************************************"
[1] "* sNMF K = 5 repetition 3 *"
[1] "*************************************"
summary of the options:
-n (number of individuals) 50
-L (number of loci) 400
-K (number of ancestral pops) 5
-x (input file) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/masked/genotypes_I.geno
-q (individual admixture file) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K5/run3/genotypes_r3.5.Q
-g (ancestral frequencies file) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K5/run3/genotypes_r3.5.G
-i (number max of iterations) 200
-a (regularization parameter) 10
-s (seed random init) 1663831666
-e (tolerance error) 1E-05
-p (number of processes) 1
- diploid
Read genotype file C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/masked/genotypes_I.geno: OK.
Main algorithm:
[ ]
[========================]
Number of iterations: 63
Least-square error: 5259.048248
Write individual ancestry coefficient file C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K5/run3/genotypes_r3.5.Q: OK.
Write ancestral allele frequency coefficient file C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K5/run3/genotypes_r3.5.G: OK.
[1] "*************************************"
[1] "* cross-entropy estimation *"
[1] "*************************************"
summary of the options:
-n (number of individuals) 50
-L (number of loci) 400
-K (number of ancestral pops) 5
-x (genotype file) C:\Users\biocbuild\bbs-3.5-bioc\meat\LEA.Rcheck\examples_i386\genotypes.geno
-q (individual admixture) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K5/run3/genotypes_r3.5.Q
-g (ancestral frequencies) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K5/run3/genotypes_r3.5.G
-i (with masked genotypes) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/masked/genotypes_I.geno
- diploid
Cross-Entropy (all data): 0.432539
Cross-Entropy (masked data): 0.602969
The project is saved into :
genotypes.snmfProject
To load the project, use:
project = load.snmfProject("genotypes.snmfProject")
To remove the project, use:
remove.snmfProject("genotypes.snmfProject")
[1] "*************************************"
[1] "* sNMF K = 6 repetition 3 *"
[1] "*************************************"
summary of the options:
-n (number of individuals) 50
-L (number of loci) 400
-K (number of ancestral pops) 6
-x (input file) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/masked/genotypes_I.geno
-q (individual admixture file) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K6/run3/genotypes_r3.6.Q
-g (ancestral frequencies file) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K6/run3/genotypes_r3.6.G
-i (number max of iterations) 200
-a (regularization parameter) 10
-s (seed random init) 1663831666
-e (tolerance error) 1E-05
-p (number of processes) 1
- diploid
Read genotype file C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/masked/genotypes_I.geno: OK.
Main algorithm:
[ ]
[==============================]
Number of iterations: 81
Least-square error: 5129.169735
Write individual ancestry coefficient file C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K6/run3/genotypes_r3.6.Q: OK.
Write ancestral allele frequency coefficient file C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K6/run3/genotypes_r3.6.G: OK.
[1] "*************************************"
[1] "* cross-entropy estimation *"
[1] "*************************************"
summary of the options:
-n (number of individuals) 50
-L (number of loci) 400
-K (number of ancestral pops) 6
-x (genotype file) C:\Users\biocbuild\bbs-3.5-bioc\meat\LEA.Rcheck\examples_i386\genotypes.geno
-q (individual admixture) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K6/run3/genotypes_r3.6.Q
-g (ancestral frequencies) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K6/run3/genotypes_r3.6.G
-i (with masked genotypes) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/masked/genotypes_I.geno
- diploid
Cross-Entropy (all data): 0.421767
Cross-Entropy (masked data): 0.600593
The project is saved into :
genotypes.snmfProject
To load the project, use:
project = load.snmfProject("genotypes.snmfProject")
To remove the project, use:
remove.snmfProject("genotypes.snmfProject")
[1] "*************************************"
[1] "* sNMF K = 7 repetition 3 *"
[1] "*************************************"
summary of the options:
-n (number of individuals) 50
-L (number of loci) 400
-K (number of ancestral pops) 7
-x (input file) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/masked/genotypes_I.geno
-q (individual admixture file) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K7/run3/genotypes_r3.7.Q
-g (ancestral frequencies file) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K7/run3/genotypes_r3.7.G
-i (number max of iterations) 200
-a (regularization parameter) 10
-s (seed random init) 1663831666
-e (tolerance error) 1E-05
-p (number of processes) 1
- diploid
Read genotype file C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/masked/genotypes_I.geno: OK.
Main algorithm:
[ ]
[=======]
Number of iterations: 19
Least-square error: 4968.747405
Write individual ancestry coefficient file C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K7/run3/genotypes_r3.7.Q: OK.
Write ancestral allele frequency coefficient file C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K7/run3/genotypes_r3.7.G: OK.
[1] "*************************************"
[1] "* cross-entropy estimation *"
[1] "*************************************"
summary of the options:
-n (number of individuals) 50
-L (number of loci) 400
-K (number of ancestral pops) 7
-x (genotype file) C:\Users\biocbuild\bbs-3.5-bioc\meat\LEA.Rcheck\examples_i386\genotypes.geno
-q (individual admixture) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K7/run3/genotypes_r3.7.Q
-g (ancestral frequencies) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K7/run3/genotypes_r3.7.G
-i (with masked genotypes) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/masked/genotypes_I.geno
- diploid
Cross-Entropy (all data): 0.406964
Cross-Entropy (masked data): 0.645974
The project is saved into :
genotypes.snmfProject
To load the project, use:
project = load.snmfProject("genotypes.snmfProject")
To remove the project, use:
remove.snmfProject("genotypes.snmfProject")
[1] "*************************************"
[1] "* sNMF K = 8 repetition 3 *"
[1] "*************************************"
summary of the options:
-n (number of individuals) 50
-L (number of loci) 400
-K (number of ancestral pops) 8
-x (input file) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/masked/genotypes_I.geno
-q (individual admixture file) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K8/run3/genotypes_r3.8.Q
-g (ancestral frequencies file) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K8/run3/genotypes_r3.8.G
-i (number max of iterations) 200
-a (regularization parameter) 10
-s (seed random init) 1663831666
-e (tolerance error) 1E-05
-p (number of processes) 1
- diploid
Read genotype file C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/masked/genotypes_I.geno: OK.
Main algorithm:
[ ]
[============================================================]
Number of iterations: 161
Least-square error: 4808.070216
Write individual ancestry coefficient file C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K8/run3/genotypes_r3.8.Q: OK.
Write ancestral allele frequency coefficient file C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K8/run3/genotypes_r3.8.G: OK.
[1] "*************************************"
[1] "* cross-entropy estimation *"
[1] "*************************************"
summary of the options:
-n (number of individuals) 50
-L (number of loci) 400
-K (number of ancestral pops) 8
-x (genotype file) C:\Users\biocbuild\bbs-3.5-bioc\meat\LEA.Rcheck\examples_i386\genotypes.geno
-q (individual admixture) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K8/run3/genotypes_r3.8.Q
-g (ancestral frequencies) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K8/run3/genotypes_r3.8.G
-i (with masked genotypes) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/masked/genotypes_I.geno
- diploid
Cross-Entropy (all data): 0.391754
Cross-Entropy (masked data): 0.66145
The project is saved into :
genotypes.snmfProject
To load the project, use:
project = load.snmfProject("genotypes.snmfProject")
To remove the project, use:
remove.snmfProject("genotypes.snmfProject")
[1] "*************************************"
[1] "* sNMF K = 9 repetition 3 *"
[1] "*************************************"
summary of the options:
-n (number of individuals) 50
-L (number of loci) 400
-K (number of ancestral pops) 9
-x (input file) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/masked/genotypes_I.geno
-q (individual admixture file) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K9/run3/genotypes_r3.9.Q
-g (ancestral frequencies file) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K9/run3/genotypes_r3.9.G
-i (number max of iterations) 200
-a (regularization parameter) 10
-s (seed random init) 1663831666
-e (tolerance error) 1E-05
-p (number of processes) 1
- diploid
Read genotype file C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/masked/genotypes_I.geno: OK.
Main algorithm:
[ ]
[==========]
Number of iterations: 26
Least-square error: 4665.987000
Write individual ancestry coefficient file C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K9/run3/genotypes_r3.9.Q: OK.
Write ancestral allele frequency coefficient file C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K9/run3/genotypes_r3.9.G: OK.
[1] "*************************************"
[1] "* cross-entropy estimation *"
[1] "*************************************"
summary of the options:
-n (number of individuals) 50
-L (number of loci) 400
-K (number of ancestral pops) 9
-x (genotype file) C:\Users\biocbuild\bbs-3.5-bioc\meat\LEA.Rcheck\examples_i386\genotypes.geno
-q (individual admixture) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K9/run3/genotypes_r3.9.Q
-g (ancestral frequencies) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K9/run3/genotypes_r3.9.G
-i (with masked genotypes) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/masked/genotypes_I.geno
- diploid
Cross-Entropy (all data): 0.382382
Cross-Entropy (masked data): 0.658231
The project is saved into :
genotypes.snmfProject
To load the project, use:
project = load.snmfProject("genotypes.snmfProject")
To remove the project, use:
remove.snmfProject("genotypes.snmfProject")
[1] "*************************************"
[1] "* sNMF K = 10 repetition 3 *"
[1] "*************************************"
summary of the options:
-n (number of individuals) 50
-L (number of loci) 400
-K (number of ancestral pops) 10
-x (input file) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/masked/genotypes_I.geno
-q (individual admixture file) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K10/run3/genotypes_r3.10.Q
-g (ancestral frequencies file) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K10/run3/genotypes_r3.10.G
-i (number max of iterations) 200
-a (regularization parameter) 10
-s (seed random init) 1663831666
-e (tolerance error) 1E-05
-p (number of processes) 1
- diploid
Read genotype file C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/masked/genotypes_I.geno: OK.
Main algorithm:
[ ]
[=================================]
Number of iterations: 88
Least-square error: 4558.928395
Write individual ancestry coefficient file C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K10/run3/genotypes_r3.10.Q: OK.
Write ancestral allele frequency coefficient file C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K10/run3/genotypes_r3.10.G: OK.
[1] "*************************************"
[1] "* cross-entropy estimation *"
[1] "*************************************"
summary of the options:
-n (number of individuals) 50
-L (number of loci) 400
-K (number of ancestral pops) 10
-x (genotype file) C:\Users\biocbuild\bbs-3.5-bioc\meat\LEA.Rcheck\examples_i386\genotypes.geno
-q (individual admixture) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K10/run3/genotypes_r3.10.Q
-g (ancestral frequencies) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K10/run3/genotypes_r3.10.G
-i (with masked genotypes) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/masked/genotypes_I.geno
- diploid
Cross-Entropy (all data): 0.366764
Cross-Entropy (masked data): 0.680938
The project is saved into :
genotypes.snmfProject
To load the project, use:
project = load.snmfProject("genotypes.snmfProject")
To remove the project, use:
remove.snmfProject("genotypes.snmfProject")
[1] 978228245
[1] "*************************************"
[1] "* create.dataset *"
[1] "*************************************"
summary of the options:
-n (number of individuals) 50
-L (number of loci) 400
-s (seed random init) 978228245
-r (percentage of masked data) 0.05
-x (genotype file in .geno format) C:\Users\biocbuild\bbs-3.5-bioc\meat\LEA.Rcheck\examples_i386\genotypes.geno
-o (output file in .geno format) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/masked/genotypes_I.geno
Write genotype file with masked data, C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/masked/genotypes_I.geno: OK.
[1] "*************************************"
[1] "* sNMF K = 1 repetition 4 *"
[1] "*************************************"
summary of the options:
-n (number of individuals) 50
-L (number of loci) 400
-K (number of ancestral pops) 1
-x (input file) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/masked/genotypes_I.geno
-q (individual admixture file) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K1/run4/genotypes_r4.1.Q
-g (ancestral frequencies file) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K1/run4/genotypes_r4.1.G
-i (number max of iterations) 200
-a (regularization parameter) 10
-s (seed random init) 978228245
-e (tolerance error) 1E-05
-p (number of processes) 1
- diploid
Read genotype file C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/masked/genotypes_I.geno: OK.
Main algorithm:
Least-square error: 6673.000084
Write individual ancestry coefficient file C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K1/run4/genotypes_r4.1.Q: OK.
Write ancestral allele frequency coefficient file C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K1/run4/genotypes_r4.1.G: OK.
[1] "*************************************"
[1] "* cross-entropy estimation *"
[1] "*************************************"
summary of the options:
-n (number of individuals) 50
-L (number of loci) 400
-K (number of ancestral pops) 1
-x (genotype file) C:\Users\biocbuild\bbs-3.5-bioc\meat\LEA.Rcheck\examples_i386\genotypes.geno
-q (individual admixture) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K1/run4/genotypes_r4.1.Q
-g (ancestral frequencies) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K1/run4/genotypes_r4.1.G
-i (with masked genotypes) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/masked/genotypes_I.geno
- diploid
Cross-Entropy (all data): 0.577358
Cross-Entropy (masked data): 0.653389
The project is saved into :
genotypes.snmfProject
To load the project, use:
project = load.snmfProject("genotypes.snmfProject")
To remove the project, use:
remove.snmfProject("genotypes.snmfProject")
[1] "*************************************"
[1] "* sNMF K = 2 repetition 4 *"
[1] "*************************************"
summary of the options:
-n (number of individuals) 50
-L (number of loci) 400
-K (number of ancestral pops) 2
-x (input file) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/masked/genotypes_I.geno
-q (individual admixture file) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K2/run4/genotypes_r4.2.Q
-g (ancestral frequencies file) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K2/run4/genotypes_r4.2.G
-i (number max of iterations) 200
-a (regularization parameter) 10
-s (seed random init) 978228245
-e (tolerance error) 1E-05
-p (number of processes) 1
- diploid
Read genotype file C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/masked/genotypes_I.geno: OK.
Main algorithm:
[ ]
[===================]
Number of iterations: 52
Least-square error: 6114.281447
Write individual ancestry coefficient file C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K2/run4/genotypes_r4.2.Q: OK.
Write ancestral allele frequency coefficient file C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K2/run4/genotypes_r4.2.G: OK.
[1] "*************************************"
[1] "* cross-entropy estimation *"
[1] "*************************************"
summary of the options:
-n (number of individuals) 50
-L (number of loci) 400
-K (number of ancestral pops) 2
-x (genotype file) C:\Users\biocbuild\bbs-3.5-bioc\meat\LEA.Rcheck\examples_i386\genotypes.geno
-q (individual admixture) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K2/run4/genotypes_r4.2.Q
-g (ancestral frequencies) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K2/run4/genotypes_r4.2.G
-i (with masked genotypes) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/masked/genotypes_I.geno
- diploid
Cross-Entropy (all data): 0.51922
Cross-Entropy (masked data): 0.622635
The project is saved into :
genotypes.snmfProject
To load the project, use:
project = load.snmfProject("genotypes.snmfProject")
To remove the project, use:
remove.snmfProject("genotypes.snmfProject")
[1] "*************************************"
[1] "* sNMF K = 3 repetition 4 *"
[1] "*************************************"
summary of the options:
-n (number of individuals) 50
-L (number of loci) 400
-K (number of ancestral pops) 3
-x (input file) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/masked/genotypes_I.geno
-q (individual admixture file) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K3/run4/genotypes_r4.3.Q
-g (ancestral frequencies file) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K3/run4/genotypes_r4.3.G
-i (number max of iterations) 200
-a (regularization parameter) 10
-s (seed random init) 978228245
-e (tolerance error) 1E-05
-p (number of processes) 1
- diploid
Read genotype file C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/masked/genotypes_I.geno: OK.
Main algorithm:
[ ]
[=========================]
Number of iterations: 67
Least-square error: 5686.734461
Write individual ancestry coefficient file C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K3/run4/genotypes_r4.3.Q: OK.
Write ancestral allele frequency coefficient file C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K3/run4/genotypes_r4.3.G: OK.
[1] "*************************************"
[1] "* cross-entropy estimation *"
[1] "*************************************"
summary of the options:
-n (number of individuals) 50
-L (number of loci) 400
-K (number of ancestral pops) 3
-x (genotype file) C:\Users\biocbuild\bbs-3.5-bioc\meat\LEA.Rcheck\examples_i386\genotypes.geno
-q (individual admixture) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K3/run4/genotypes_r4.3.Q
-g (ancestral frequencies) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K3/run4/genotypes_r4.3.G
-i (with masked genotypes) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/masked/genotypes_I.geno
- diploid
Cross-Entropy (all data): 0.476855
Cross-Entropy (masked data): 0.627808
The project is saved into :
genotypes.snmfProject
To load the project, use:
project = load.snmfProject("genotypes.snmfProject")
To remove the project, use:
remove.snmfProject("genotypes.snmfProject")
[1] "*************************************"
[1] "* sNMF K = 4 repetition 4 *"
[1] "*************************************"
summary of the options:
-n (number of individuals) 50
-L (number of loci) 400
-K (number of ancestral pops) 4
-x (input file) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/masked/genotypes_I.geno
-q (individual admixture file) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K4/run4/genotypes_r4.4.Q
-g (ancestral frequencies file) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K4/run4/genotypes_r4.4.G
-i (number max of iterations) 200
-a (regularization parameter) 10
-s (seed random init) 978228245
-e (tolerance error) 1E-05
-p (number of processes) 1
- diploid
Read genotype file C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/masked/genotypes_I.geno: OK.
Main algorithm:
[ ]
[======================================]
Number of iterations: 101
Least-square error: 5454.820325
Write individual ancestry coefficient file C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K4/run4/genotypes_r4.4.Q: OK.
Write ancestral allele frequency coefficient file C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K4/run4/genotypes_r4.4.G: OK.
[1] "*************************************"
[1] "* cross-entropy estimation *"
[1] "*************************************"
summary of the options:
-n (number of individuals) 50
-L (number of loci) 400
-K (number of ancestral pops) 4
-x (genotype file) C:\Users\biocbuild\bbs-3.5-bioc\meat\LEA.Rcheck\examples_i386\genotypes.geno
-q (individual admixture) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K4/run4/genotypes_r4.4.Q
-g (ancestral frequencies) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K4/run4/genotypes_r4.4.G
-i (with masked genotypes) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/masked/genotypes_I.geno
- diploid
Cross-Entropy (all data): 0.451427
Cross-Entropy (masked data): 0.62781
The project is saved into :
genotypes.snmfProject
To load the project, use:
project = load.snmfProject("genotypes.snmfProject")
To remove the project, use:
remove.snmfProject("genotypes.snmfProject")
[1] "*************************************"
[1] "* sNMF K = 5 repetition 4 *"
[1] "*************************************"
summary of the options:
-n (number of individuals) 50
-L (number of loci) 400
-K (number of ancestral pops) 5
-x (input file) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/masked/genotypes_I.geno
-q (individual admixture file) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K5/run4/genotypes_r4.5.Q
-g (ancestral frequencies file) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K5/run4/genotypes_r4.5.G
-i (number max of iterations) 200
-a (regularization parameter) 10
-s (seed random init) 978228245
-e (tolerance error) 1E-05
-p (number of processes) 1
- diploid
Read genotype file C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/masked/genotypes_I.geno: OK.
Main algorithm:
[ ]
[========================]
Number of iterations: 64
Least-square error: 5246.630287
Write individual ancestry coefficient file C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K5/run4/genotypes_r4.5.Q: OK.
Write ancestral allele frequency coefficient file C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K5/run4/genotypes_r4.5.G: OK.
[1] "*************************************"
[1] "* cross-entropy estimation *"
[1] "*************************************"
summary of the options:
-n (number of individuals) 50
-L (number of loci) 400
-K (number of ancestral pops) 5
-x (genotype file) C:\Users\biocbuild\bbs-3.5-bioc\meat\LEA.Rcheck\examples_i386\genotypes.geno
-q (individual admixture) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K5/run4/genotypes_r4.5.Q
-g (ancestral frequencies) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K5/run4/genotypes_r4.5.G
-i (with masked genotypes) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/masked/genotypes_I.geno
- diploid
Cross-Entropy (all data): 0.431562
Cross-Entropy (masked data): 0.656121
The project is saved into :
genotypes.snmfProject
To load the project, use:
project = load.snmfProject("genotypes.snmfProject")
To remove the project, use:
remove.snmfProject("genotypes.snmfProject")
[1] "*************************************"
[1] "* sNMF K = 6 repetition 4 *"
[1] "*************************************"
summary of the options:
-n (number of individuals) 50
-L (number of loci) 400
-K (number of ancestral pops) 6
-x (input file) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/masked/genotypes_I.geno
-q (individual admixture file) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K6/run4/genotypes_r4.6.Q
-g (ancestral frequencies file) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K6/run4/genotypes_r4.6.G
-i (number max of iterations) 200
-a (regularization parameter) 10
-s (seed random init) 978228245
-e (tolerance error) 1E-05
-p (number of processes) 1
- diploid
Read genotype file C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/masked/genotypes_I.geno: OK.
Main algorithm:
[ ]
[====================]
Number of iterations: 53
Least-square error: 5061.904811
Write individual ancestry coefficient file C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K6/run4/genotypes_r4.6.Q: OK.
Write ancestral allele frequency coefficient file C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K6/run4/genotypes_r4.6.G: OK.
[1] "*************************************"
[1] "* cross-entropy estimation *"
[1] "*************************************"
summary of the options:
-n (number of individuals) 50
-L (number of loci) 400
-K (number of ancestral pops) 6
-x (genotype file) C:\Users\biocbuild\bbs-3.5-bioc\meat\LEA.Rcheck\examples_i386\genotypes.geno
-q (individual admixture) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K6/run4/genotypes_r4.6.Q
-g (ancestral frequencies) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K6/run4/genotypes_r4.6.G
-i (with masked genotypes) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/masked/genotypes_I.geno
- diploid
Cross-Entropy (all data): 0.419145
Cross-Entropy (masked data): 0.648032
The project is saved into :
genotypes.snmfProject
To load the project, use:
project = load.snmfProject("genotypes.snmfProject")
To remove the project, use:
remove.snmfProject("genotypes.snmfProject")
[1] "*************************************"
[1] "* sNMF K = 7 repetition 4 *"
[1] "*************************************"
summary of the options:
-n (number of individuals) 50
-L (number of loci) 400
-K (number of ancestral pops) 7
-x (input file) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/masked/genotypes_I.geno
-q (individual admixture file) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K7/run4/genotypes_r4.7.Q
-g (ancestral frequencies file) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K7/run4/genotypes_r4.7.G
-i (number max of iterations) 200
-a (regularization parameter) 10
-s (seed random init) 978228245
-e (tolerance error) 1E-05
-p (number of processes) 1
- diploid
Read genotype file C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/masked/genotypes_I.geno: OK.
Main algorithm:
[ ]
[=================]
Number of iterations: 45
Least-square error: 4900.905752
Write individual ancestry coefficient file C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K7/run4/genotypes_r4.7.Q: OK.
Write ancestral allele frequency coefficient file C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K7/run4/genotypes_r4.7.G: OK.
[1] "*************************************"
[1] "* cross-entropy estimation *"
[1] "*************************************"
summary of the options:
-n (number of individuals) 50
-L (number of loci) 400
-K (number of ancestral pops) 7
-x (genotype file) C:\Users\biocbuild\bbs-3.5-bioc\meat\LEA.Rcheck\examples_i386\genotypes.geno
-q (individual admixture) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K7/run4/genotypes_r4.7.Q
-g (ancestral frequencies) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K7/run4/genotypes_r4.7.G
-i (with masked genotypes) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/masked/genotypes_I.geno
- diploid
Cross-Entropy (all data): 0.402564
Cross-Entropy (masked data): 0.670979
The project is saved into :
genotypes.snmfProject
To load the project, use:
project = load.snmfProject("genotypes.snmfProject")
To remove the project, use:
remove.snmfProject("genotypes.snmfProject")
[1] "*************************************"
[1] "* sNMF K = 8 repetition 4 *"
[1] "*************************************"
summary of the options:
-n (number of individuals) 50
-L (number of loci) 400
-K (number of ancestral pops) 8
-x (input file) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/masked/genotypes_I.geno
-q (individual admixture file) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K8/run4/genotypes_r4.8.Q
-g (ancestral frequencies file) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K8/run4/genotypes_r4.8.G
-i (number max of iterations) 200
-a (regularization parameter) 10
-s (seed random init) 978228245
-e (tolerance error) 1E-05
-p (number of processes) 1
- diploid
Read genotype file C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/masked/genotypes_I.geno: OK.
Main algorithm:
[ ]
[================================================]
Number of iterations: 128
Least-square error: 4770.546261
Write individual ancestry coefficient file C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K8/run4/genotypes_r4.8.Q: OK.
Write ancestral allele frequency coefficient file C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K8/run4/genotypes_r4.8.G: OK.
[1] "*************************************"
[1] "* cross-entropy estimation *"
[1] "*************************************"
summary of the options:
-n (number of individuals) 50
-L (number of loci) 400
-K (number of ancestral pops) 8
-x (genotype file) C:\Users\biocbuild\bbs-3.5-bioc\meat\LEA.Rcheck\examples_i386\genotypes.geno
-q (individual admixture) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K8/run4/genotypes_r4.8.Q
-g (ancestral frequencies) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K8/run4/genotypes_r4.8.G
-i (with masked genotypes) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/masked/genotypes_I.geno
- diploid
Cross-Entropy (all data): 0.388788
Cross-Entropy (masked data): 0.704105
The project is saved into :
genotypes.snmfProject
To load the project, use:
project = load.snmfProject("genotypes.snmfProject")
To remove the project, use:
remove.snmfProject("genotypes.snmfProject")
[1] "*************************************"
[1] "* sNMF K = 9 repetition 4 *"
[1] "*************************************"
summary of the options:
-n (number of individuals) 50
-L (number of loci) 400
-K (number of ancestral pops) 9
-x (input file) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/masked/genotypes_I.geno
-q (individual admixture file) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K9/run4/genotypes_r4.9.Q
-g (ancestral frequencies file) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K9/run4/genotypes_r4.9.G
-i (number max of iterations) 200
-a (regularization parameter) 10
-s (seed random init) 978228245
-e (tolerance error) 1E-05
-p (number of processes) 1
- diploid
Read genotype file C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/masked/genotypes_I.geno: OK.
Main algorithm:
[ ]
[===============]
Number of iterations: 39
Least-square error: 4657.859291
Write individual ancestry coefficient file C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K9/run4/genotypes_r4.9.Q: OK.
Write ancestral allele frequency coefficient file C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K9/run4/genotypes_r4.9.G: OK.
[1] "*************************************"
[1] "* cross-entropy estimation *"
[1] "*************************************"
summary of the options:
-n (number of individuals) 50
-L (number of loci) 400
-K (number of ancestral pops) 9
-x (genotype file) C:\Users\biocbuild\bbs-3.5-bioc\meat\LEA.Rcheck\examples_i386\genotypes.geno
-q (individual admixture) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K9/run4/genotypes_r4.9.Q
-g (ancestral frequencies) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K9/run4/genotypes_r4.9.G
-i (with masked genotypes) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/masked/genotypes_I.geno
- diploid
Cross-Entropy (all data): 0.380486
Cross-Entropy (masked data): 0.741667
The project is saved into :
genotypes.snmfProject
To load the project, use:
project = load.snmfProject("genotypes.snmfProject")
To remove the project, use:
remove.snmfProject("genotypes.snmfProject")
[1] "*************************************"
[1] "* sNMF K = 10 repetition 4 *"
[1] "*************************************"
summary of the options:
-n (number of individuals) 50
-L (number of loci) 400
-K (number of ancestral pops) 10
-x (input file) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/masked/genotypes_I.geno
-q (individual admixture file) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K10/run4/genotypes_r4.10.Q
-g (ancestral frequencies file) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K10/run4/genotypes_r4.10.G
-i (number max of iterations) 200
-a (regularization parameter) 10
-s (seed random init) 978228245
-e (tolerance error) 1E-05
-p (number of processes) 1
- diploid
Read genotype file C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/masked/genotypes_I.geno: OK.
Main algorithm:
[ ]
[==============================]
Number of iterations: 79
Least-square error: 4507.925502
Write individual ancestry coefficient file C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K10/run4/genotypes_r4.10.Q: OK.
Write ancestral allele frequency coefficient file C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K10/run4/genotypes_r4.10.G: OK.
[1] "*************************************"
[1] "* cross-entropy estimation *"
[1] "*************************************"
summary of the options:
-n (number of individuals) 50
-L (number of loci) 400
-K (number of ancestral pops) 10
-x (genotype file) C:\Users\biocbuild\bbs-3.5-bioc\meat\LEA.Rcheck\examples_i386\genotypes.geno
-q (individual admixture) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K10/run4/genotypes_r4.10.Q
-g (ancestral frequencies) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K10/run4/genotypes_r4.10.G
-i (with masked genotypes) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/masked/genotypes_I.geno
- diploid
Cross-Entropy (all data): 0.368642
Cross-Entropy (masked data): 0.770849
The project is saved into :
genotypes.snmfProject
To load the project, use:
project = load.snmfProject("genotypes.snmfProject")
To remove the project, use:
remove.snmfProject("genotypes.snmfProject")
[1] 1112635313
[1] "*************************************"
[1] "* create.dataset *"
[1] "*************************************"
summary of the options:
-n (number of individuals) 50
-L (number of loci) 400
-s (seed random init) 1112635313
-r (percentage of masked data) 0.05
-x (genotype file in .geno format) C:\Users\biocbuild\bbs-3.5-bioc\meat\LEA.Rcheck\examples_i386\genotypes.geno
-o (output file in .geno format) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/masked/genotypes_I.geno
Write genotype file with masked data, C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/masked/genotypes_I.geno: OK.
[1] "*************************************"
[1] "* sNMF K = 1 repetition 5 *"
[1] "*************************************"
summary of the options:
-n (number of individuals) 50
-L (number of loci) 400
-K (number of ancestral pops) 1
-x (input file) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/masked/genotypes_I.geno
-q (individual admixture file) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K1/run5/genotypes_r5.1.Q
-g (ancestral frequencies file) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K1/run5/genotypes_r5.1.G
-i (number max of iterations) 200
-a (regularization parameter) 10
-s (seed random init) 1112635313
-e (tolerance error) 1E-05
-p (number of processes) 1
- diploid
Read genotype file C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/masked/genotypes_I.geno: OK.
Main algorithm:
Least-square error: 6675.560081
Write individual ancestry coefficient file C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K1/run5/genotypes_r5.1.Q: OK.
Write ancestral allele frequency coefficient file C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K1/run5/genotypes_r5.1.G: OK.
[1] "*************************************"
[1] "* cross-entropy estimation *"
[1] "*************************************"
summary of the options:
-n (number of individuals) 50
-L (number of loci) 400
-K (number of ancestral pops) 1
-x (genotype file) C:\Users\biocbuild\bbs-3.5-bioc\meat\LEA.Rcheck\examples_i386\genotypes.geno
-q (individual admixture) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K1/run5/genotypes_r5.1.Q
-g (ancestral frequencies) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K1/run5/genotypes_r5.1.G
-i (with masked genotypes) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/masked/genotypes_I.geno
- diploid
Cross-Entropy (all data): 0.577574
Cross-Entropy (masked data): 0.628905
The project is saved into :
genotypes.snmfProject
To load the project, use:
project = load.snmfProject("genotypes.snmfProject")
To remove the project, use:
remove.snmfProject("genotypes.snmfProject")
[1] "*************************************"
[1] "* sNMF K = 2 repetition 5 *"
[1] "*************************************"
summary of the options:
-n (number of individuals) 50
-L (number of loci) 400
-K (number of ancestral pops) 2
-x (input file) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/masked/genotypes_I.geno
-q (individual admixture file) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K2/run5/genotypes_r5.2.Q
-g (ancestral frequencies file) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K2/run5/genotypes_r5.2.G
-i (number max of iterations) 200
-a (regularization parameter) 10
-s (seed random init) 1112635313
-e (tolerance error) 1E-05
-p (number of processes) 1
- diploid
Read genotype file C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/masked/genotypes_I.geno: OK.
Main algorithm:
[ ]
[=======]
Number of iterations: 20
Least-square error: 6134.969795
Write individual ancestry coefficient file C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K2/run5/genotypes_r5.2.Q: OK.
Write ancestral allele frequency coefficient file C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K2/run5/genotypes_r5.2.G: OK.
[1] "*************************************"
[1] "* cross-entropy estimation *"
[1] "*************************************"
summary of the options:
-n (number of individuals) 50
-L (number of loci) 400
-K (number of ancestral pops) 2
-x (genotype file) C:\Users\biocbuild\bbs-3.5-bioc\meat\LEA.Rcheck\examples_i386\genotypes.geno
-q (individual admixture) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K2/run5/genotypes_r5.2.Q
-g (ancestral frequencies) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K2/run5/genotypes_r5.2.G
-i (with masked genotypes) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/masked/genotypes_I.geno
- diploid
Cross-Entropy (all data): 0.51933
Cross-Entropy (masked data): 0.615149
The project is saved into :
genotypes.snmfProject
To load the project, use:
project = load.snmfProject("genotypes.snmfProject")
To remove the project, use:
remove.snmfProject("genotypes.snmfProject")
[1] "*************************************"
[1] "* sNMF K = 3 repetition 5 *"
[1] "*************************************"
summary of the options:
-n (number of individuals) 50
-L (number of loci) 400
-K (number of ancestral pops) 3
-x (input file) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/masked/genotypes_I.geno
-q (individual admixture file) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K3/run5/genotypes_r5.3.Q
-g (ancestral frequencies file) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K3/run5/genotypes_r5.3.G
-i (number max of iterations) 200
-a (regularization parameter) 10
-s (seed random init) 1112635313
-e (tolerance error) 1E-05
-p (number of processes) 1
- diploid
Read genotype file C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/masked/genotypes_I.geno: OK.
Main algorithm:
[ ]
[==============================]
Number of iterations: 80
Least-square error: 5730.954230
Write individual ancestry coefficient file C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K3/run5/genotypes_r5.3.Q: OK.
Write ancestral allele frequency coefficient file C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K3/run5/genotypes_r5.3.G: OK.
[1] "*************************************"
[1] "* cross-entropy estimation *"
[1] "*************************************"
summary of the options:
-n (number of individuals) 50
-L (number of loci) 400
-K (number of ancestral pops) 3
-x (genotype file) C:\Users\biocbuild\bbs-3.5-bioc\meat\LEA.Rcheck\examples_i386\genotypes.geno
-q (individual admixture) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K3/run5/genotypes_r5.3.Q
-g (ancestral frequencies) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K3/run5/genotypes_r5.3.G
-i (with masked genotypes) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/masked/genotypes_I.geno
- diploid
Cross-Entropy (all data): 0.478454
Cross-Entropy (masked data): 0.579509
The project is saved into :
genotypes.snmfProject
To load the project, use:
project = load.snmfProject("genotypes.snmfProject")
To remove the project, use:
remove.snmfProject("genotypes.snmfProject")
[1] "*************************************"
[1] "* sNMF K = 4 repetition 5 *"
[1] "*************************************"
summary of the options:
-n (number of individuals) 50
-L (number of loci) 400
-K (number of ancestral pops) 4
-x (input file) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/masked/genotypes_I.geno
-q (individual admixture file) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K4/run5/genotypes_r5.4.Q
-g (ancestral frequencies file) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K4/run5/genotypes_r5.4.G
-i (number max of iterations) 200
-a (regularization parameter) 10
-s (seed random init) 1112635313
-e (tolerance error) 1E-05
-p (number of processes) 1
- diploid
Read genotype file C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/masked/genotypes_I.geno: OK.
Main algorithm:
[ ]
[===========]
Number of iterations: 30
Least-square error: 5451.612124
Write individual ancestry coefficient file C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K4/run5/genotypes_r5.4.Q: OK.
Write ancestral allele frequency coefficient file C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K4/run5/genotypes_r5.4.G: OK.
[1] "*************************************"
[1] "* cross-entropy estimation *"
[1] "*************************************"
summary of the options:
-n (number of individuals) 50
-L (number of loci) 400
-K (number of ancestral pops) 4
-x (genotype file) C:\Users\biocbuild\bbs-3.5-bioc\meat\LEA.Rcheck\examples_i386\genotypes.geno
-q (individual admixture) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K4/run5/genotypes_r5.4.Q
-g (ancestral frequencies) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K4/run5/genotypes_r5.4.G
-i (with masked genotypes) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/masked/genotypes_I.geno
- diploid
Cross-Entropy (all data): 0.450918
Cross-Entropy (masked data): 0.592771
The project is saved into :
genotypes.snmfProject
To load the project, use:
project = load.snmfProject("genotypes.snmfProject")
To remove the project, use:
remove.snmfProject("genotypes.snmfProject")
[1] "*************************************"
[1] "* sNMF K = 5 repetition 5 *"
[1] "*************************************"
summary of the options:
-n (number of individuals) 50
-L (number of loci) 400
-K (number of ancestral pops) 5
-x (input file) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/masked/genotypes_I.geno
-q (individual admixture file) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K5/run5/genotypes_r5.5.Q
-g (ancestral frequencies file) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K5/run5/genotypes_r5.5.G
-i (number max of iterations) 200
-a (regularization parameter) 10
-s (seed random init) 1112635313
-e (tolerance error) 1E-05
-p (number of processes) 1
- diploid
Read genotype file C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/masked/genotypes_I.geno: OK.
Main algorithm:
[ ]
[=====================]
Number of iterations: 57
Least-square error: 5252.047014
Write individual ancestry coefficient file C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K5/run5/genotypes_r5.5.Q: OK.
Write ancestral allele frequency coefficient file C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K5/run5/genotypes_r5.5.G: OK.
[1] "*************************************"
[1] "* cross-entropy estimation *"
[1] "*************************************"
summary of the options:
-n (number of individuals) 50
-L (number of loci) 400
-K (number of ancestral pops) 5
-x (genotype file) C:\Users\biocbuild\bbs-3.5-bioc\meat\LEA.Rcheck\examples_i386\genotypes.geno
-q (individual admixture) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K5/run5/genotypes_r5.5.Q
-g (ancestral frequencies) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K5/run5/genotypes_r5.5.G
-i (with masked genotypes) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/masked/genotypes_I.geno
- diploid
Cross-Entropy (all data): 0.431065
Cross-Entropy (masked data): 0.593079
The project is saved into :
genotypes.snmfProject
To load the project, use:
project = load.snmfProject("genotypes.snmfProject")
To remove the project, use:
remove.snmfProject("genotypes.snmfProject")
[1] "*************************************"
[1] "* sNMF K = 6 repetition 5 *"
[1] "*************************************"
summary of the options:
-n (number of individuals) 50
-L (number of loci) 400
-K (number of ancestral pops) 6
-x (input file) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/masked/genotypes_I.geno
-q (individual admixture file) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K6/run5/genotypes_r5.6.Q
-g (ancestral frequencies file) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K6/run5/genotypes_r5.6.G
-i (number max of iterations) 200
-a (regularization parameter) 10
-s (seed random init) 1112635313
-e (tolerance error) 1E-05
-p (number of processes) 1
- diploid
Read genotype file C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/masked/genotypes_I.geno: OK.
Main algorithm:
[ ]
[==========================]
Number of iterations: 70
Least-square error: 5112.304118
Write individual ancestry coefficient file C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K6/run5/genotypes_r5.6.Q: OK.
Write ancestral allele frequency coefficient file C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K6/run5/genotypes_r5.6.G: OK.
[1] "*************************************"
[1] "* cross-entropy estimation *"
[1] "*************************************"
summary of the options:
-n (number of individuals) 50
-L (number of loci) 400
-K (number of ancestral pops) 6
-x (genotype file) C:\Users\biocbuild\bbs-3.5-bioc\meat\LEA.Rcheck\examples_i386\genotypes.geno
-q (individual admixture) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K6/run5/genotypes_r5.6.Q
-g (ancestral frequencies) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K6/run5/genotypes_r5.6.G
-i (with masked genotypes) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/masked/genotypes_I.geno
- diploid
Cross-Entropy (all data): 0.416691
Cross-Entropy (masked data): 0.626546
The project is saved into :
genotypes.snmfProject
To load the project, use:
project = load.snmfProject("genotypes.snmfProject")
To remove the project, use:
remove.snmfProject("genotypes.snmfProject")
[1] "*************************************"
[1] "* sNMF K = 7 repetition 5 *"
[1] "*************************************"
summary of the options:
-n (number of individuals) 50
-L (number of loci) 400
-K (number of ancestral pops) 7
-x (input file) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/masked/genotypes_I.geno
-q (individual admixture file) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K7/run5/genotypes_r5.7.Q
-g (ancestral frequencies file) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K7/run5/genotypes_r5.7.G
-i (number max of iterations) 200
-a (regularization parameter) 10
-s (seed random init) 1112635313
-e (tolerance error) 1E-05
-p (number of processes) 1
- diploid
Read genotype file C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/masked/genotypes_I.geno: OK.
Main algorithm:
[ ]
[=======================================]
Number of iterations: 105
Least-square error: 4926.048671
Write individual ancestry coefficient file C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K7/run5/genotypes_r5.7.Q: OK.
Write ancestral allele frequency coefficient file C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K7/run5/genotypes_r5.7.G: OK.
[1] "*************************************"
[1] "* cross-entropy estimation *"
[1] "*************************************"
summary of the options:
-n (number of individuals) 50
-L (number of loci) 400
-K (number of ancestral pops) 7
-x (genotype file) C:\Users\biocbuild\bbs-3.5-bioc\meat\LEA.Rcheck\examples_i386\genotypes.geno
-q (individual admixture) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K7/run5/genotypes_r5.7.Q
-g (ancestral frequencies) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K7/run5/genotypes_r5.7.G
-i (with masked genotypes) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/masked/genotypes_I.geno
- diploid
Cross-Entropy (all data): 0.401294
Cross-Entropy (masked data): 0.606972
The project is saved into :
genotypes.snmfProject
To load the project, use:
project = load.snmfProject("genotypes.snmfProject")
To remove the project, use:
remove.snmfProject("genotypes.snmfProject")
[1] "*************************************"
[1] "* sNMF K = 8 repetition 5 *"
[1] "*************************************"
summary of the options:
-n (number of individuals) 50
-L (number of loci) 400
-K (number of ancestral pops) 8
-x (input file) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/masked/genotypes_I.geno
-q (individual admixture file) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K8/run5/genotypes_r5.8.Q
-g (ancestral frequencies file) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K8/run5/genotypes_r5.8.G
-i (number max of iterations) 200
-a (regularization parameter) 10
-s (seed random init) 1112635313
-e (tolerance error) 1E-05
-p (number of processes) 1
- diploid
Read genotype file C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/masked/genotypes_I.geno: OK.
Main algorithm:
[ ]
[=====================================]
Number of iterations: 100
Least-square error: 4798.119007
Write individual ancestry coefficient file C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K8/run5/genotypes_r5.8.Q: OK.
Write ancestral allele frequency coefficient file C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K8/run5/genotypes_r5.8.G: OK.
[1] "*************************************"
[1] "* cross-entropy estimation *"
[1] "*************************************"
summary of the options:
-n (number of individuals) 50
-L (number of loci) 400
-K (number of ancestral pops) 8
-x (genotype file) C:\Users\biocbuild\bbs-3.5-bioc\meat\LEA.Rcheck\examples_i386\genotypes.geno
-q (individual admixture) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K8/run5/genotypes_r5.8.Q
-g (ancestral frequencies) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K8/run5/genotypes_r5.8.G
-i (with masked genotypes) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/masked/genotypes_I.geno
- diploid
Cross-Entropy (all data): 0.391412
Cross-Entropy (masked data): 0.649503
The project is saved into :
genotypes.snmfProject
To load the project, use:
project = load.snmfProject("genotypes.snmfProject")
To remove the project, use:
remove.snmfProject("genotypes.snmfProject")
[1] "*************************************"
[1] "* sNMF K = 9 repetition 5 *"
[1] "*************************************"
summary of the options:
-n (number of individuals) 50
-L (number of loci) 400
-K (number of ancestral pops) 9
-x (input file) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/masked/genotypes_I.geno
-q (individual admixture file) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K9/run5/genotypes_r5.9.Q
-g (ancestral frequencies file) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K9/run5/genotypes_r5.9.G
-i (number max of iterations) 200
-a (regularization parameter) 10
-s (seed random init) 1112635313
-e (tolerance error) 1E-05
-p (number of processes) 1
- diploid
Read genotype file C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/masked/genotypes_I.geno: OK.
Main algorithm:
[ ]
[===================]
Number of iterations: 50
Least-square error: 4694.241247
Write individual ancestry coefficient file C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K9/run5/genotypes_r5.9.Q: OK.
Write ancestral allele frequency coefficient file C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K9/run5/genotypes_r5.9.G: OK.
[1] "*************************************"
[1] "* cross-entropy estimation *"
[1] "*************************************"
summary of the options:
-n (number of individuals) 50
-L (number of loci) 400
-K (number of ancestral pops) 9
-x (genotype file) C:\Users\biocbuild\bbs-3.5-bioc\meat\LEA.Rcheck\examples_i386\genotypes.geno
-q (individual admixture) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K9/run5/genotypes_r5.9.Q
-g (ancestral frequencies) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K9/run5/genotypes_r5.9.G
-i (with masked genotypes) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/masked/genotypes_I.geno
- diploid
Cross-Entropy (all data): 0.382776
Cross-Entropy (masked data): 0.707923
The project is saved into :
genotypes.snmfProject
To load the project, use:
project = load.snmfProject("genotypes.snmfProject")
To remove the project, use:
remove.snmfProject("genotypes.snmfProject")
[1] "*************************************"
[1] "* sNMF K = 10 repetition 5 *"
[1] "*************************************"
summary of the options:
-n (number of individuals) 50
-L (number of loci) 400
-K (number of ancestral pops) 10
-x (input file) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/masked/genotypes_I.geno
-q (individual admixture file) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K10/run5/genotypes_r5.10.Q
-g (ancestral frequencies file) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K10/run5/genotypes_r5.10.G
-i (number max of iterations) 200
-a (regularization parameter) 10
-s (seed random init) 1112635313
-e (tolerance error) 1E-05
-p (number of processes) 1
- diploid
Read genotype file C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/masked/genotypes_I.geno: OK.
Main algorithm:
[ ]
[===========================================================================]
Number of iterations: 200
Least-square error: 4486.695926
Write individual ancestry coefficient file C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K10/run5/genotypes_r5.10.Q: OK.
Write ancestral allele frequency coefficient file C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K10/run5/genotypes_r5.10.G: OK.
[1] "*************************************"
[1] "* cross-entropy estimation *"
[1] "*************************************"
summary of the options:
-n (number of individuals) 50
-L (number of loci) 400
-K (number of ancestral pops) 10
-x (genotype file) C:\Users\biocbuild\bbs-3.5-bioc\meat\LEA.Rcheck\examples_i386\genotypes.geno
-q (individual admixture) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K10/run5/genotypes_r5.10.Q
-g (ancestral frequencies) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K10/run5/genotypes_r5.10.G
-i (with masked genotypes) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/masked/genotypes_I.geno
- diploid
Cross-Entropy (all data): 0.365973
Cross-Entropy (masked data): 0.75422
The project is saved into :
genotypes.snmfProject
To load the project, use:
project = load.snmfProject("genotypes.snmfProject")
To remove the project, use:
remove.snmfProject("genotypes.snmfProject")
[1] 2118848436
[1] "*************************************"
[1] "* create.dataset *"
[1] "*************************************"
summary of the options:
-n (number of individuals) 50
-L (number of loci) 400
-s (seed random init) 2118848436
-r (percentage of masked data) 0.05
-x (genotype file in .geno format) C:\Users\biocbuild\bbs-3.5-bioc\meat\LEA.Rcheck\examples_i386\genotypes.geno
-o (output file in .geno format) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/masked/genotypes_I.geno
Write genotype file with masked data, C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/masked/genotypes_I.geno: OK.
[1] "*************************************"
[1] "* sNMF K = 1 repetition 6 *"
[1] "*************************************"
summary of the options:
-n (number of individuals) 50
-L (number of loci) 400
-K (number of ancestral pops) 1
-x (input file) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/masked/genotypes_I.geno
-q (individual admixture file) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K1/run6/genotypes_r6.1.Q
-g (ancestral frequencies file) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K1/run6/genotypes_r6.1.G
-i (number max of iterations) 200
-a (regularization parameter) 10
-s (seed random init) 2118848436
-e (tolerance error) 1E-05
-p (number of processes) 1
- diploid
Read genotype file C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/masked/genotypes_I.geno: OK.
Main algorithm:
Least-square error: 6686.760083
Write individual ancestry coefficient file C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K1/run6/genotypes_r6.1.Q: OK.
Write ancestral allele frequency coefficient file C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K1/run6/genotypes_r6.1.G: OK.
[1] "*************************************"
[1] "* cross-entropy estimation *"
[1] "*************************************"
summary of the options:
-n (number of individuals) 50
-L (number of loci) 400
-K (number of ancestral pops) 1
-x (genotype file) C:\Users\biocbuild\bbs-3.5-bioc\meat\LEA.Rcheck\examples_i386\genotypes.geno
-q (individual admixture) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K1/run6/genotypes_r6.1.Q
-g (ancestral frequencies) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K1/run6/genotypes_r6.1.G
-i (with masked genotypes) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/masked/genotypes_I.geno
- diploid
Cross-Entropy (all data): 0.578209
Cross-Entropy (masked data): 0.632533
The project is saved into :
genotypes.snmfProject
To load the project, use:
project = load.snmfProject("genotypes.snmfProject")
To remove the project, use:
remove.snmfProject("genotypes.snmfProject")
[1] "*************************************"
[1] "* sNMF K = 2 repetition 6 *"
[1] "*************************************"
summary of the options:
-n (number of individuals) 50
-L (number of loci) 400
-K (number of ancestral pops) 2
-x (input file) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/masked/genotypes_I.geno
-q (individual admixture file) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K2/run6/genotypes_r6.2.Q
-g (ancestral frequencies file) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K2/run6/genotypes_r6.2.G
-i (number max of iterations) 200
-a (regularization parameter) 10
-s (seed random init) 2118848436
-e (tolerance error) 1E-05
-p (number of processes) 1
- diploid
Read genotype file C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/masked/genotypes_I.geno: OK.
Main algorithm:
[ ]
[=================]
Number of iterations: 46
Least-square error: 6146.261309
Write individual ancestry coefficient file C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K2/run6/genotypes_r6.2.Q: OK.
Write ancestral allele frequency coefficient file C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K2/run6/genotypes_r6.2.G: OK.
[1] "*************************************"
[1] "* cross-entropy estimation *"
[1] "*************************************"
summary of the options:
-n (number of individuals) 50
-L (number of loci) 400
-K (number of ancestral pops) 2
-x (genotype file) C:\Users\biocbuild\bbs-3.5-bioc\meat\LEA.Rcheck\examples_i386\genotypes.geno
-q (individual admixture) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K2/run6/genotypes_r6.2.Q
-g (ancestral frequencies) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K2/run6/genotypes_r6.2.G
-i (with masked genotypes) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/masked/genotypes_I.geno
- diploid
Cross-Entropy (all data): 0.520973
Cross-Entropy (masked data): 0.588781
The project is saved into :
genotypes.snmfProject
To load the project, use:
project = load.snmfProject("genotypes.snmfProject")
To remove the project, use:
remove.snmfProject("genotypes.snmfProject")
[1] "*************************************"
[1] "* sNMF K = 3 repetition 6 *"
[1] "*************************************"
summary of the options:
-n (number of individuals) 50
-L (number of loci) 400
-K (number of ancestral pops) 3
-x (input file) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/masked/genotypes_I.geno
-q (individual admixture file) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K3/run6/genotypes_r6.3.Q
-g (ancestral frequencies file) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K3/run6/genotypes_r6.3.G
-i (number max of iterations) 200
-a (regularization parameter) 10
-s (seed random init) 2118848436
-e (tolerance error) 1E-05
-p (number of processes) 1
- diploid
Read genotype file C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/masked/genotypes_I.geno: OK.
Main algorithm:
[ ]
[================================]
Number of iterations: 85
Least-square error: 5750.472128
Write individual ancestry coefficient file C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K3/run6/genotypes_r6.3.Q: OK.
Write ancestral allele frequency coefficient file C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K3/run6/genotypes_r6.3.G: OK.
[1] "*************************************"
[1] "* cross-entropy estimation *"
[1] "*************************************"
summary of the options:
-n (number of individuals) 50
-L (number of loci) 400
-K (number of ancestral pops) 3
-x (genotype file) C:\Users\biocbuild\bbs-3.5-bioc\meat\LEA.Rcheck\examples_i386\genotypes.geno
-q (individual admixture) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K3/run6/genotypes_r6.3.Q
-g (ancestral frequencies) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K3/run6/genotypes_r6.3.G
-i (with masked genotypes) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/masked/genotypes_I.geno
- diploid
Cross-Entropy (all data): 0.480875
Cross-Entropy (masked data): 0.562483
The project is saved into :
genotypes.snmfProject
To load the project, use:
project = load.snmfProject("genotypes.snmfProject")
To remove the project, use:
remove.snmfProject("genotypes.snmfProject")
[1] "*************************************"
[1] "* sNMF K = 4 repetition 6 *"
[1] "*************************************"
summary of the options:
-n (number of individuals) 50
-L (number of loci) 400
-K (number of ancestral pops) 4
-x (input file) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/masked/genotypes_I.geno
-q (individual admixture file) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K4/run6/genotypes_r6.4.Q
-g (ancestral frequencies file) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K4/run6/genotypes_r6.4.G
-i (number max of iterations) 200
-a (regularization parameter) 10
-s (seed random init) 2118848436
-e (tolerance error) 1E-05
-p (number of processes) 1
- diploid
Read genotype file C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/masked/genotypes_I.geno: OK.
Main algorithm:
[ ]
[========================]
Number of iterations: 64
Least-square error: 5478.770122
Write individual ancestry coefficient file C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K4/run6/genotypes_r6.4.Q: OK.
Write ancestral allele frequency coefficient file C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K4/run6/genotypes_r6.4.G: OK.
[1] "*************************************"
[1] "* cross-entropy estimation *"
[1] "*************************************"
summary of the options:
-n (number of individuals) 50
-L (number of loci) 400
-K (number of ancestral pops) 4
-x (genotype file) C:\Users\biocbuild\bbs-3.5-bioc\meat\LEA.Rcheck\examples_i386\genotypes.geno
-q (individual admixture) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K4/run6/genotypes_r6.4.Q
-g (ancestral frequencies) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K4/run6/genotypes_r6.4.G
-i (with masked genotypes) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/masked/genotypes_I.geno
- diploid
Cross-Entropy (all data): 0.453501
Cross-Entropy (masked data): 0.554297
The project is saved into :
genotypes.snmfProject
To load the project, use:
project = load.snmfProject("genotypes.snmfProject")
To remove the project, use:
remove.snmfProject("genotypes.snmfProject")
[1] "*************************************"
[1] "* sNMF K = 5 repetition 6 *"
[1] "*************************************"
summary of the options:
-n (number of individuals) 50
-L (number of loci) 400
-K (number of ancestral pops) 5
-x (input file) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/masked/genotypes_I.geno
-q (individual admixture file) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K5/run6/genotypes_r6.5.Q
-g (ancestral frequencies file) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K5/run6/genotypes_r6.5.G
-i (number max of iterations) 200
-a (regularization parameter) 10
-s (seed random init) 2118848436
-e (tolerance error) 1E-05
-p (number of processes) 1
- diploid
Read genotype file C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/masked/genotypes_I.geno: OK.
Main algorithm:
[ ]
[==================================]
Number of iterations: 92
Least-square error: 5299.379087
Write individual ancestry coefficient file C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K5/run6/genotypes_r6.5.Q: OK.
Write ancestral allele frequency coefficient file C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K5/run6/genotypes_r6.5.G: OK.
[1] "*************************************"
[1] "* cross-entropy estimation *"
[1] "*************************************"
summary of the options:
-n (number of individuals) 50
-L (number of loci) 400
-K (number of ancestral pops) 5
-x (genotype file) C:\Users\biocbuild\bbs-3.5-bioc\meat\LEA.Rcheck\examples_i386\genotypes.geno
-q (individual admixture) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K5/run6/genotypes_r6.5.Q
-g (ancestral frequencies) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K5/run6/genotypes_r6.5.G
-i (with masked genotypes) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/masked/genotypes_I.geno
- diploid
Cross-Entropy (all data): 0.435402
Cross-Entropy (masked data): 0.551378
The project is saved into :
genotypes.snmfProject
To load the project, use:
project = load.snmfProject("genotypes.snmfProject")
To remove the project, use:
remove.snmfProject("genotypes.snmfProject")
[1] "*************************************"
[1] "* sNMF K = 6 repetition 6 *"
[1] "*************************************"
summary of the options:
-n (number of individuals) 50
-L (number of loci) 400
-K (number of ancestral pops) 6
-x (input file) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/masked/genotypes_I.geno
-q (individual admixture file) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K6/run6/genotypes_r6.6.Q
-g (ancestral frequencies file) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K6/run6/genotypes_r6.6.G
-i (number max of iterations) 200
-a (regularization parameter) 10
-s (seed random init) 2118848436
-e (tolerance error) 1E-05
-p (number of processes) 1
- diploid
Read genotype file C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/masked/genotypes_I.geno: OK.
Main algorithm:
[ ]
[============]
Number of iterations: 33
Least-square error: 5135.419284
Write individual ancestry coefficient file C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K6/run6/genotypes_r6.6.Q: OK.
Write ancestral allele frequency coefficient file C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K6/run6/genotypes_r6.6.G: OK.
[1] "*************************************"
[1] "* cross-entropy estimation *"
[1] "*************************************"
summary of the options:
-n (number of individuals) 50
-L (number of loci) 400
-K (number of ancestral pops) 6
-x (genotype file) C:\Users\biocbuild\bbs-3.5-bioc\meat\LEA.Rcheck\examples_i386\genotypes.geno
-q (individual admixture) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K6/run6/genotypes_r6.6.Q
-g (ancestral frequencies) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K6/run6/genotypes_r6.6.G
-i (with masked genotypes) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/masked/genotypes_I.geno
- diploid
Cross-Entropy (all data): 0.423341
Cross-Entropy (masked data): 0.570034
The project is saved into :
genotypes.snmfProject
To load the project, use:
project = load.snmfProject("genotypes.snmfProject")
To remove the project, use:
remove.snmfProject("genotypes.snmfProject")
[1] "*************************************"
[1] "* sNMF K = 7 repetition 6 *"
[1] "*************************************"
summary of the options:
-n (number of individuals) 50
-L (number of loci) 400
-K (number of ancestral pops) 7
-x (input file) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/masked/genotypes_I.geno
-q (individual admixture file) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K7/run6/genotypes_r6.7.Q
-g (ancestral frequencies file) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K7/run6/genotypes_r6.7.G
-i (number max of iterations) 200
-a (regularization parameter) 10
-s (seed random init) 2118848436
-e (tolerance error) 1E-05
-p (number of processes) 1
- diploid
Read genotype file C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/masked/genotypes_I.geno: OK.
Main algorithm:
[ ]
[===============]
Number of iterations: 40
Least-square error: 4956.520445
Write individual ancestry coefficient file C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K7/run6/genotypes_r6.7.Q: OK.
Write ancestral allele frequency coefficient file C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K7/run6/genotypes_r6.7.G: OK.
[1] "*************************************"
[1] "* cross-entropy estimation *"
[1] "*************************************"
summary of the options:
-n (number of individuals) 50
-L (number of loci) 400
-K (number of ancestral pops) 7
-x (genotype file) C:\Users\biocbuild\bbs-3.5-bioc\meat\LEA.Rcheck\examples_i386\genotypes.geno
-q (individual admixture) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K7/run6/genotypes_r6.7.Q
-g (ancestral frequencies) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K7/run6/genotypes_r6.7.G
-i (with masked genotypes) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/masked/genotypes_I.geno
- diploid
Cross-Entropy (all data): 0.407417
Cross-Entropy (masked data): 0.610368
The project is saved into :
genotypes.snmfProject
To load the project, use:
project = load.snmfProject("genotypes.snmfProject")
To remove the project, use:
remove.snmfProject("genotypes.snmfProject")
[1] "*************************************"
[1] "* sNMF K = 8 repetition 6 *"
[1] "*************************************"
summary of the options:
-n (number of individuals) 50
-L (number of loci) 400
-K (number of ancestral pops) 8
-x (input file) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/masked/genotypes_I.geno
-q (individual admixture file) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K8/run6/genotypes_r6.8.Q
-g (ancestral frequencies file) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K8/run6/genotypes_r6.8.G
-i (number max of iterations) 200
-a (regularization parameter) 10
-s (seed random init) 2118848436
-e (tolerance error) 1E-05
-p (number of processes) 1
- diploid
Read genotype file C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/masked/genotypes_I.geno: OK.
Main algorithm:
[ ]
[===============]
Number of iterations: 40
Least-square error: 4827.425675
Write individual ancestry coefficient file C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K8/run6/genotypes_r6.8.Q: OK.
Write ancestral allele frequency coefficient file C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K8/run6/genotypes_r6.8.G: OK.
[1] "*************************************"
[1] "* cross-entropy estimation *"
[1] "*************************************"
summary of the options:
-n (number of individuals) 50
-L (number of loci) 400
-K (number of ancestral pops) 8
-x (genotype file) C:\Users\biocbuild\bbs-3.5-bioc\meat\LEA.Rcheck\examples_i386\genotypes.geno
-q (individual admixture) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K8/run6/genotypes_r6.8.Q
-g (ancestral frequencies) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K8/run6/genotypes_r6.8.G
-i (with masked genotypes) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/masked/genotypes_I.geno
- diploid
Cross-Entropy (all data): 0.393576
Cross-Entropy (masked data): 0.608405
The project is saved into :
genotypes.snmfProject
To load the project, use:
project = load.snmfProject("genotypes.snmfProject")
To remove the project, use:
remove.snmfProject("genotypes.snmfProject")
[1] "*************************************"
[1] "* sNMF K = 9 repetition 6 *"
[1] "*************************************"
summary of the options:
-n (number of individuals) 50
-L (number of loci) 400
-K (number of ancestral pops) 9
-x (input file) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/masked/genotypes_I.geno
-q (individual admixture file) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K9/run6/genotypes_r6.9.Q
-g (ancestral frequencies file) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K9/run6/genotypes_r6.9.G
-i (number max of iterations) 200
-a (regularization parameter) 10
-s (seed random init) 2118848436
-e (tolerance error) 1E-05
-p (number of processes) 1
- diploid
Read genotype file C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/masked/genotypes_I.geno: OK.
Main algorithm:
[ ]
[===================================================]
Number of iterations: 137
Least-square error: 4654.967069
Write individual ancestry coefficient file C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K9/run6/genotypes_r6.9.Q: OK.
Write ancestral allele frequency coefficient file C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K9/run6/genotypes_r6.9.G: OK.
[1] "*************************************"
[1] "* cross-entropy estimation *"
[1] "*************************************"
summary of the options:
-n (number of individuals) 50
-L (number of loci) 400
-K (number of ancestral pops) 9
-x (genotype file) C:\Users\biocbuild\bbs-3.5-bioc\meat\LEA.Rcheck\examples_i386\genotypes.geno
-q (individual admixture) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K9/run6/genotypes_r6.9.Q
-g (ancestral frequencies) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K9/run6/genotypes_r6.9.G
-i (with masked genotypes) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/masked/genotypes_I.geno
- diploid
Cross-Entropy (all data): 0.380524
Cross-Entropy (masked data): 0.65942
The project is saved into :
genotypes.snmfProject
To load the project, use:
project = load.snmfProject("genotypes.snmfProject")
To remove the project, use:
remove.snmfProject("genotypes.snmfProject")
[1] "*************************************"
[1] "* sNMF K = 10 repetition 6 *"
[1] "*************************************"
summary of the options:
-n (number of individuals) 50
-L (number of loci) 400
-K (number of ancestral pops) 10
-x (input file) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/masked/genotypes_I.geno
-q (individual admixture file) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K10/run6/genotypes_r6.10.Q
-g (ancestral frequencies file) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K10/run6/genotypes_r6.10.G
-i (number max of iterations) 200
-a (regularization parameter) 10
-s (seed random init) 2118848436
-e (tolerance error) 1E-05
-p (number of processes) 1
- diploid
Read genotype file C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/masked/genotypes_I.geno: OK.
Main algorithm:
[ ]
[===================]
Number of iterations: 50
Least-square error: 4570.317548
Write individual ancestry coefficient file C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K10/run6/genotypes_r6.10.Q: OK.
Write ancestral allele frequency coefficient file C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K10/run6/genotypes_r6.10.G: OK.
[1] "*************************************"
[1] "* cross-entropy estimation *"
[1] "*************************************"
summary of the options:
-n (number of individuals) 50
-L (number of loci) 400
-K (number of ancestral pops) 10
-x (genotype file) C:\Users\biocbuild\bbs-3.5-bioc\meat\LEA.Rcheck\examples_i386\genotypes.geno
-q (individual admixture) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K10/run6/genotypes_r6.10.Q
-g (ancestral frequencies) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K10/run6/genotypes_r6.10.G
-i (with masked genotypes) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/masked/genotypes_I.geno
- diploid
Cross-Entropy (all data): 0.37029
Cross-Entropy (masked data): 0.670867
The project is saved into :
genotypes.snmfProject
To load the project, use:
project = load.snmfProject("genotypes.snmfProject")
To remove the project, use:
remove.snmfProject("genotypes.snmfProject")
[1] 1105185580
[1] "*************************************"
[1] "* create.dataset *"
[1] "*************************************"
summary of the options:
-n (number of individuals) 50
-L (number of loci) 400
-s (seed random init) 1105185580
-r (percentage of masked data) 0.05
-x (genotype file in .geno format) C:\Users\biocbuild\bbs-3.5-bioc\meat\LEA.Rcheck\examples_i386\genotypes.geno
-o (output file in .geno format) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/masked/genotypes_I.geno
Write genotype file with masked data, C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/masked/genotypes_I.geno: OK.
[1] "*************************************"
[1] "* sNMF K = 1 repetition 7 *"
[1] "*************************************"
summary of the options:
-n (number of individuals) 50
-L (number of loci) 400
-K (number of ancestral pops) 1
-x (input file) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/masked/genotypes_I.geno
-q (individual admixture file) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K1/run7/genotypes_r7.1.Q
-g (ancestral frequencies file) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K1/run7/genotypes_r7.1.G
-i (number max of iterations) 200
-a (regularization parameter) 10
-s (seed random init) 1105185580
-e (tolerance error) 1E-05
-p (number of processes) 1
- diploid
Read genotype file C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/masked/genotypes_I.geno: OK.
Main algorithm:
Least-square error: 6672.520081
Write individual ancestry coefficient file C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K1/run7/genotypes_r7.1.Q: OK.
Write ancestral allele frequency coefficient file C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K1/run7/genotypes_r7.1.G: OK.
[1] "*************************************"
[1] "* cross-entropy estimation *"
[1] "*************************************"
summary of the options:
-n (number of individuals) 50
-L (number of loci) 400
-K (number of ancestral pops) 1
-x (genotype file) C:\Users\biocbuild\bbs-3.5-bioc\meat\LEA.Rcheck\examples_i386\genotypes.geno
-q (individual admixture) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K1/run7/genotypes_r7.1.Q
-g (ancestral frequencies) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K1/run7/genotypes_r7.1.G
-i (with masked genotypes) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/masked/genotypes_I.geno
- diploid
Cross-Entropy (all data): 0.577923
Cross-Entropy (masked data): 0.621984
The project is saved into :
genotypes.snmfProject
To load the project, use:
project = load.snmfProject("genotypes.snmfProject")
To remove the project, use:
remove.snmfProject("genotypes.snmfProject")
[1] "*************************************"
[1] "* sNMF K = 2 repetition 7 *"
[1] "*************************************"
summary of the options:
-n (number of individuals) 50
-L (number of loci) 400
-K (number of ancestral pops) 2
-x (input file) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/masked/genotypes_I.geno
-q (individual admixture file) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K2/run7/genotypes_r7.2.Q
-g (ancestral frequencies file) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K2/run7/genotypes_r7.2.G
-i (number max of iterations) 200
-a (regularization parameter) 10
-s (seed random init) 1105185580
-e (tolerance error) 1E-05
-p (number of processes) 1
- diploid
Read genotype file C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/masked/genotypes_I.geno: OK.
Main algorithm:
[ ]
[===============]
Number of iterations: 39
Least-square error: 6130.022354
Write individual ancestry coefficient file C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K2/run7/genotypes_r7.2.Q: OK.
Write ancestral allele frequency coefficient file C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K2/run7/genotypes_r7.2.G: OK.
[1] "*************************************"
[1] "* cross-entropy estimation *"
[1] "*************************************"
summary of the options:
-n (number of individuals) 50
-L (number of loci) 400
-K (number of ancestral pops) 2
-x (genotype file) C:\Users\biocbuild\bbs-3.5-bioc\meat\LEA.Rcheck\examples_i386\genotypes.geno
-q (individual admixture) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K2/run7/genotypes_r7.2.Q
-g (ancestral frequencies) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K2/run7/genotypes_r7.2.G
-i (with masked genotypes) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/masked/genotypes_I.geno
- diploid
Cross-Entropy (all data): 0.520674
Cross-Entropy (masked data): 0.578427
The project is saved into :
genotypes.snmfProject
To load the project, use:
project = load.snmfProject("genotypes.snmfProject")
To remove the project, use:
remove.snmfProject("genotypes.snmfProject")
[1] "*************************************"
[1] "* sNMF K = 3 repetition 7 *"
[1] "*************************************"
summary of the options:
-n (number of individuals) 50
-L (number of loci) 400
-K (number of ancestral pops) 3
-x (input file) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/masked/genotypes_I.geno
-q (individual admixture file) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K3/run7/genotypes_r7.3.Q
-g (ancestral frequencies file) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K3/run7/genotypes_r7.3.G
-i (number max of iterations) 200
-a (regularization parameter) 10
-s (seed random init) 1105185580
-e (tolerance error) 1E-05
-p (number of processes) 1
- diploid
Read genotype file C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/masked/genotypes_I.geno: OK.
Main algorithm:
[ ]
[=====================]
Number of iterations: 57
Least-square error: 5710.284434
Write individual ancestry coefficient file C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K3/run7/genotypes_r7.3.Q: OK.
Write ancestral allele frequency coefficient file C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K3/run7/genotypes_r7.3.G: OK.
[1] "*************************************"
[1] "* cross-entropy estimation *"
[1] "*************************************"
summary of the options:
-n (number of individuals) 50
-L (number of loci) 400
-K (number of ancestral pops) 3
-x (genotype file) C:\Users\biocbuild\bbs-3.5-bioc\meat\LEA.Rcheck\examples_i386\genotypes.geno
-q (individual admixture) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K3/run7/genotypes_r7.3.Q
-g (ancestral frequencies) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K3/run7/genotypes_r7.3.G
-i (with masked genotypes) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/masked/genotypes_I.geno
- diploid
Cross-Entropy (all data): 0.478206
Cross-Entropy (masked data): 0.569239
The project is saved into :
genotypes.snmfProject
To load the project, use:
project = load.snmfProject("genotypes.snmfProject")
To remove the project, use:
remove.snmfProject("genotypes.snmfProject")
[1] "*************************************"
[1] "* sNMF K = 4 repetition 7 *"
[1] "*************************************"
summary of the options:
-n (number of individuals) 50
-L (number of loci) 400
-K (number of ancestral pops) 4
-x (input file) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/masked/genotypes_I.geno
-q (individual admixture file) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K4/run7/genotypes_r7.4.Q
-g (ancestral frequencies file) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K4/run7/genotypes_r7.4.G
-i (number max of iterations) 200
-a (regularization parameter) 10
-s (seed random init) 1105185580
-e (tolerance error) 1E-05
-p (number of processes) 1
- diploid
Read genotype file C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/masked/genotypes_I.geno: OK.
Main algorithm:
[ ]
[=======================================]
Number of iterations: 105
Least-square error: 5459.121429
Write individual ancestry coefficient file C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K4/run7/genotypes_r7.4.Q: OK.
Write ancestral allele frequency coefficient file C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K4/run7/genotypes_r7.4.G: OK.
[1] "*************************************"
[1] "* cross-entropy estimation *"
[1] "*************************************"
summary of the options:
-n (number of individuals) 50
-L (number of loci) 400
-K (number of ancestral pops) 4
-x (genotype file) C:\Users\biocbuild\bbs-3.5-bioc\meat\LEA.Rcheck\examples_i386\genotypes.geno
-q (individual admixture) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K4/run7/genotypes_r7.4.Q
-g (ancestral frequencies) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K4/run7/genotypes_r7.4.G
-i (with masked genotypes) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/masked/genotypes_I.geno
- diploid
Cross-Entropy (all data): 0.452129
Cross-Entropy (masked data): 0.566386
The project is saved into :
genotypes.snmfProject
To load the project, use:
project = load.snmfProject("genotypes.snmfProject")
To remove the project, use:
remove.snmfProject("genotypes.snmfProject")
[1] "*************************************"
[1] "* sNMF K = 5 repetition 7 *"
[1] "*************************************"
summary of the options:
-n (number of individuals) 50
-L (number of loci) 400
-K (number of ancestral pops) 5
-x (input file) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/masked/genotypes_I.geno
-q (individual admixture file) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K5/run7/genotypes_r7.5.Q
-g (ancestral frequencies file) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K5/run7/genotypes_r7.5.G
-i (number max of iterations) 200
-a (regularization parameter) 10
-s (seed random init) 1105185580
-e (tolerance error) 1E-05
-p (number of processes) 1
- diploid
Read genotype file C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/masked/genotypes_I.geno: OK.
Main algorithm:
[ ]
[===========================]
Number of iterations: 73
Least-square error: 5273.645342
Write individual ancestry coefficient file C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K5/run7/genotypes_r7.5.Q: OK.
Write ancestral allele frequency coefficient file C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K5/run7/genotypes_r7.5.G: OK.
[1] "*************************************"
[1] "* cross-entropy estimation *"
[1] "*************************************"
summary of the options:
-n (number of individuals) 50
-L (number of loci) 400
-K (number of ancestral pops) 5
-x (genotype file) C:\Users\biocbuild\bbs-3.5-bioc\meat\LEA.Rcheck\examples_i386\genotypes.geno
-q (individual admixture) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K5/run7/genotypes_r7.5.Q
-g (ancestral frequencies) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K5/run7/genotypes_r7.5.G
-i (with masked genotypes) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/masked/genotypes_I.geno
- diploid
Cross-Entropy (all data): 0.434223
Cross-Entropy (masked data): 0.606016
The project is saved into :
genotypes.snmfProject
To load the project, use:
project = load.snmfProject("genotypes.snmfProject")
To remove the project, use:
remove.snmfProject("genotypes.snmfProject")
[1] "*************************************"
[1] "* sNMF K = 6 repetition 7 *"
[1] "*************************************"
summary of the options:
-n (number of individuals) 50
-L (number of loci) 400
-K (number of ancestral pops) 6
-x (input file) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/masked/genotypes_I.geno
-q (individual admixture file) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K6/run7/genotypes_r7.6.Q
-g (ancestral frequencies file) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K6/run7/genotypes_r7.6.G
-i (number max of iterations) 200
-a (regularization parameter) 10
-s (seed random init) 1105185580
-e (tolerance error) 1E-05
-p (number of processes) 1
- diploid
Read genotype file C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/masked/genotypes_I.geno: OK.
Main algorithm:
[ ]
[==============================================]
Number of iterations: 123
Least-square error: 5090.375677
Write individual ancestry coefficient file C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K6/run7/genotypes_r7.6.Q: OK.
Write ancestral allele frequency coefficient file C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K6/run7/genotypes_r7.6.G: OK.
[1] "*************************************"
[1] "* cross-entropy estimation *"
[1] "*************************************"
summary of the options:
-n (number of individuals) 50
-L (number of loci) 400
-K (number of ancestral pops) 6
-x (genotype file) C:\Users\biocbuild\bbs-3.5-bioc\meat\LEA.Rcheck\examples_i386\genotypes.geno
-q (individual admixture) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K6/run7/genotypes_r7.6.Q
-g (ancestral frequencies) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K6/run7/genotypes_r7.6.G
-i (with masked genotypes) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/masked/genotypes_I.geno
- diploid
Cross-Entropy (all data): 0.418233
Cross-Entropy (masked data): 0.610178
The project is saved into :
genotypes.snmfProject
To load the project, use:
project = load.snmfProject("genotypes.snmfProject")
To remove the project, use:
remove.snmfProject("genotypes.snmfProject")
[1] "*************************************"
[1] "* sNMF K = 7 repetition 7 *"
[1] "*************************************"
summary of the options:
-n (number of individuals) 50
-L (number of loci) 400
-K (number of ancestral pops) 7
-x (input file) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/masked/genotypes_I.geno
-q (individual admixture file) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K7/run7/genotypes_r7.7.Q
-g (ancestral frequencies file) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K7/run7/genotypes_r7.7.G
-i (number max of iterations) 200
-a (regularization parameter) 10
-s (seed random init) 1105185580
-e (tolerance error) 1E-05
-p (number of processes) 1
- diploid
Read genotype file C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/masked/genotypes_I.geno: OK.
Main algorithm:
[ ]
[===================]
Number of iterations: 51
Least-square error: 4938.070185
Write individual ancestry coefficient file C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K7/run7/genotypes_r7.7.Q: OK.
Write ancestral allele frequency coefficient file C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K7/run7/genotypes_r7.7.G: OK.
[1] "*************************************"
[1] "* cross-entropy estimation *"
[1] "*************************************"
summary of the options:
-n (number of individuals) 50
-L (number of loci) 400
-K (number of ancestral pops) 7
-x (genotype file) C:\Users\biocbuild\bbs-3.5-bioc\meat\LEA.Rcheck\examples_i386\genotypes.geno
-q (individual admixture) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K7/run7/genotypes_r7.7.Q
-g (ancestral frequencies) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K7/run7/genotypes_r7.7.G
-i (with masked genotypes) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/masked/genotypes_I.geno
- diploid
Cross-Entropy (all data): 0.405361
Cross-Entropy (masked data): 0.677745
The project is saved into :
genotypes.snmfProject
To load the project, use:
project = load.snmfProject("genotypes.snmfProject")
To remove the project, use:
remove.snmfProject("genotypes.snmfProject")
[1] "*************************************"
[1] "* sNMF K = 8 repetition 7 *"
[1] "*************************************"
summary of the options:
-n (number of individuals) 50
-L (number of loci) 400
-K (number of ancestral pops) 8
-x (input file) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/masked/genotypes_I.geno
-q (individual admixture file) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K8/run7/genotypes_r7.8.Q
-g (ancestral frequencies file) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K8/run7/genotypes_r7.8.G
-i (number max of iterations) 200
-a (regularization parameter) 10
-s (seed random init) 1105185580
-e (tolerance error) 1E-05
-p (number of processes) 1
- diploid
Read genotype file C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/masked/genotypes_I.geno: OK.
Main algorithm:
[ ]
[=============================================]
Number of iterations: 120
Least-square error: 4759.121187
Write individual ancestry coefficient file C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K8/run7/genotypes_r7.8.Q: OK.
Write ancestral allele frequency coefficient file C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K8/run7/genotypes_r7.8.G: OK.
[1] "*************************************"
[1] "* cross-entropy estimation *"
[1] "*************************************"
summary of the options:
-n (number of individuals) 50
-L (number of loci) 400
-K (number of ancestral pops) 8
-x (genotype file) C:\Users\biocbuild\bbs-3.5-bioc\meat\LEA.Rcheck\examples_i386\genotypes.geno
-q (individual admixture) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K8/run7/genotypes_r7.8.Q
-g (ancestral frequencies) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K8/run7/genotypes_r7.8.G
-i (with masked genotypes) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/masked/genotypes_I.geno
- diploid
Cross-Entropy (all data): 0.388719
Cross-Entropy (masked data): 0.680652
The project is saved into :
genotypes.snmfProject
To load the project, use:
project = load.snmfProject("genotypes.snmfProject")
To remove the project, use:
remove.snmfProject("genotypes.snmfProject")
[1] "*************************************"
[1] "* sNMF K = 9 repetition 7 *"
[1] "*************************************"
summary of the options:
-n (number of individuals) 50
-L (number of loci) 400
-K (number of ancestral pops) 9
-x (input file) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/masked/genotypes_I.geno
-q (individual admixture file) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K9/run7/genotypes_r7.9.Q
-g (ancestral frequencies file) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K9/run7/genotypes_r7.9.G
-i (number max of iterations) 200
-a (regularization parameter) 10
-s (seed random init) 1105185580
-e (tolerance error) 1E-05
-p (number of processes) 1
- diploid
Read genotype file C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/masked/genotypes_I.geno: OK.
Main algorithm:
[ ]
[==================================]
Number of iterations: 90
Least-square error: 4625.866493
Write individual ancestry coefficient file C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K9/run7/genotypes_r7.9.Q: OK.
Write ancestral allele frequency coefficient file C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K9/run7/genotypes_r7.9.G: OK.
[1] "*************************************"
[1] "* cross-entropy estimation *"
[1] "*************************************"
summary of the options:
-n (number of individuals) 50
-L (number of loci) 400
-K (number of ancestral pops) 9
-x (genotype file) C:\Users\biocbuild\bbs-3.5-bioc\meat\LEA.Rcheck\examples_i386\genotypes.geno
-q (individual admixture) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K9/run7/genotypes_r7.9.Q
-g (ancestral frequencies) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K9/run7/genotypes_r7.9.G
-i (with masked genotypes) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/masked/genotypes_I.geno
- diploid
Cross-Entropy (all data): 0.377566
Cross-Entropy (masked data): 0.708889
The project is saved into :
genotypes.snmfProject
To load the project, use:
project = load.snmfProject("genotypes.snmfProject")
To remove the project, use:
remove.snmfProject("genotypes.snmfProject")
[1] "*************************************"
[1] "* sNMF K = 10 repetition 7 *"
[1] "*************************************"
summary of the options:
-n (number of individuals) 50
-L (number of loci) 400
-K (number of ancestral pops) 10
-x (input file) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/masked/genotypes_I.geno
-q (individual admixture file) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K10/run7/genotypes_r7.10.Q
-g (ancestral frequencies file) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K10/run7/genotypes_r7.10.G
-i (number max of iterations) 200
-a (regularization parameter) 10
-s (seed random init) 1105185580
-e (tolerance error) 1E-05
-p (number of processes) 1
- diploid
Read genotype file C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/masked/genotypes_I.geno: OK.
Main algorithm:
[ ]
[===========================]
Number of iterations: 73
Least-square error: 4484.872473
Write individual ancestry coefficient file C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K10/run7/genotypes_r7.10.Q: OK.
Write ancestral allele frequency coefficient file C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K10/run7/genotypes_r7.10.G: OK.
[1] "*************************************"
[1] "* cross-entropy estimation *"
[1] "*************************************"
summary of the options:
-n (number of individuals) 50
-L (number of loci) 400
-K (number of ancestral pops) 10
-x (genotype file) C:\Users\biocbuild\bbs-3.5-bioc\meat\LEA.Rcheck\examples_i386\genotypes.geno
-q (individual admixture) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K10/run7/genotypes_r7.10.Q
-g (ancestral frequencies) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K10/run7/genotypes_r7.10.G
-i (with masked genotypes) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/masked/genotypes_I.geno
- diploid
Cross-Entropy (all data): 0.366894
Cross-Entropy (masked data): 0.738775
The project is saved into :
genotypes.snmfProject
To load the project, use:
project = load.snmfProject("genotypes.snmfProject")
To remove the project, use:
remove.snmfProject("genotypes.snmfProject")
[1] 1947026275
[1] "*************************************"
[1] "* create.dataset *"
[1] "*************************************"
summary of the options:
-n (number of individuals) 50
-L (number of loci) 400
-s (seed random init) 1947026275
-r (percentage of masked data) 0.05
-x (genotype file in .geno format) C:\Users\biocbuild\bbs-3.5-bioc\meat\LEA.Rcheck\examples_i386\genotypes.geno
-o (output file in .geno format) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/masked/genotypes_I.geno
Write genotype file with masked data, C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/masked/genotypes_I.geno: OK.
[1] "*************************************"
[1] "* sNMF K = 1 repetition 8 *"
[1] "*************************************"
summary of the options:
-n (number of individuals) 50
-L (number of loci) 400
-K (number of ancestral pops) 1
-x (input file) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/masked/genotypes_I.geno
-q (individual admixture file) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K1/run8/genotypes_r8.1.Q
-g (ancestral frequencies file) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K1/run8/genotypes_r8.1.G
-i (number max of iterations) 200
-a (regularization parameter) 10
-s (seed random init) 1947026275
-e (tolerance error) 1E-05
-p (number of processes) 1
- diploid
Read genotype file C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/masked/genotypes_I.geno: OK.
Main algorithm:
Least-square error: 6682.080084
Write individual ancestry coefficient file C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K1/run8/genotypes_r8.1.Q: OK.
Write ancestral allele frequency coefficient file C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K1/run8/genotypes_r8.1.G: OK.
[1] "*************************************"
[1] "* cross-entropy estimation *"
[1] "*************************************"
summary of the options:
-n (number of individuals) 50
-L (number of loci) 400
-K (number of ancestral pops) 1
-x (genotype file) C:\Users\biocbuild\bbs-3.5-bioc\meat\LEA.Rcheck\examples_i386\genotypes.geno
-q (individual admixture) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K1/run8/genotypes_r8.1.Q
-g (ancestral frequencies) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K1/run8/genotypes_r8.1.G
-i (with masked genotypes) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/masked/genotypes_I.geno
- diploid
Cross-Entropy (all data): 0.576431
Cross-Entropy (masked data): 0.664931
The project is saved into :
genotypes.snmfProject
To load the project, use:
project = load.snmfProject("genotypes.snmfProject")
To remove the project, use:
remove.snmfProject("genotypes.snmfProject")
[1] "*************************************"
[1] "* sNMF K = 2 repetition 8 *"
[1] "*************************************"
summary of the options:
-n (number of individuals) 50
-L (number of loci) 400
-K (number of ancestral pops) 2
-x (input file) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/masked/genotypes_I.geno
-q (individual admixture file) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K2/run8/genotypes_r8.2.Q
-g (ancestral frequencies file) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K2/run8/genotypes_r8.2.G
-i (number max of iterations) 200
-a (regularization parameter) 10
-s (seed random init) 1947026275
-e (tolerance error) 1E-05
-p (number of processes) 1
- diploid
Read genotype file C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/masked/genotypes_I.geno: OK.
Main algorithm:
[ ]
[=========]
Number of iterations: 24
Least-square error: 6094.215615
Write individual ancestry coefficient file C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K2/run8/genotypes_r8.2.Q: OK.
Write ancestral allele frequency coefficient file C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K2/run8/genotypes_r8.2.G: OK.
[1] "*************************************"
[1] "* cross-entropy estimation *"
[1] "*************************************"
summary of the options:
-n (number of individuals) 50
-L (number of loci) 400
-K (number of ancestral pops) 2
-x (genotype file) C:\Users\biocbuild\bbs-3.5-bioc\meat\LEA.Rcheck\examples_i386\genotypes.geno
-q (individual admixture) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K2/run8/genotypes_r8.2.Q
-g (ancestral frequencies) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K2/run8/genotypes_r8.2.G
-i (with masked genotypes) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/masked/genotypes_I.geno
- diploid
Cross-Entropy (all data): 0.518042
Cross-Entropy (masked data): 0.638326
The project is saved into :
genotypes.snmfProject
To load the project, use:
project = load.snmfProject("genotypes.snmfProject")
To remove the project, use:
remove.snmfProject("genotypes.snmfProject")
[1] "*************************************"
[1] "* sNMF K = 3 repetition 8 *"
[1] "*************************************"
summary of the options:
-n (number of individuals) 50
-L (number of loci) 400
-K (number of ancestral pops) 3
-x (input file) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/masked/genotypes_I.geno
-q (individual admixture file) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K3/run8/genotypes_r8.3.Q
-g (ancestral frequencies file) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K3/run8/genotypes_r8.3.G
-i (number max of iterations) 200
-a (regularization parameter) 10
-s (seed random init) 1947026275
-e (tolerance error) 1E-05
-p (number of processes) 1
- diploid
Read genotype file C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/masked/genotypes_I.geno: OK.
Main algorithm:
[ ]
[======================]
Number of iterations: 58
Least-square error: 5695.797934
Write individual ancestry coefficient file C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K3/run8/genotypes_r8.3.Q: OK.
Write ancestral allele frequency coefficient file C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K3/run8/genotypes_r8.3.G: OK.
[1] "*************************************"
[1] "* cross-entropy estimation *"
[1] "*************************************"
summary of the options:
-n (number of individuals) 50
-L (number of loci) 400
-K (number of ancestral pops) 3
-x (genotype file) C:\Users\biocbuild\bbs-3.5-bioc\meat\LEA.Rcheck\examples_i386\genotypes.geno
-q (individual admixture) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K3/run8/genotypes_r8.3.Q
-g (ancestral frequencies) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K3/run8/genotypes_r8.3.G
-i (with masked genotypes) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/masked/genotypes_I.geno
- diploid
Cross-Entropy (all data): 0.477289
Cross-Entropy (masked data): 0.607649
The project is saved into :
genotypes.snmfProject
To load the project, use:
project = load.snmfProject("genotypes.snmfProject")
To remove the project, use:
remove.snmfProject("genotypes.snmfProject")
[1] "*************************************"
[1] "* sNMF K = 4 repetition 8 *"
[1] "*************************************"
summary of the options:
-n (number of individuals) 50
-L (number of loci) 400
-K (number of ancestral pops) 4
-x (input file) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/masked/genotypes_I.geno
-q (individual admixture file) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K4/run8/genotypes_r8.4.Q
-g (ancestral frequencies file) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K4/run8/genotypes_r8.4.G
-i (number max of iterations) 200
-a (regularization parameter) 10
-s (seed random init) 1947026275
-e (tolerance error) 1E-05
-p (number of processes) 1
- diploid
Read genotype file C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/masked/genotypes_I.geno: OK.
Main algorithm:
[ ]
[=======================]
Number of iterations: 61
Least-square error: 5434.037653
Write individual ancestry coefficient file C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K4/run8/genotypes_r8.4.Q: OK.
Write ancestral allele frequency coefficient file C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K4/run8/genotypes_r8.4.G: OK.
[1] "*************************************"
[1] "* cross-entropy estimation *"
[1] "*************************************"
summary of the options:
-n (number of individuals) 50
-L (number of loci) 400
-K (number of ancestral pops) 4
-x (genotype file) C:\Users\biocbuild\bbs-3.5-bioc\meat\LEA.Rcheck\examples_i386\genotypes.geno
-q (individual admixture) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K4/run8/genotypes_r8.4.Q
-g (ancestral frequencies) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K4/run8/genotypes_r8.4.G
-i (with masked genotypes) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/masked/genotypes_I.geno
- diploid
Cross-Entropy (all data): 0.450727
Cross-Entropy (masked data): 0.619342
The project is saved into :
genotypes.snmfProject
To load the project, use:
project = load.snmfProject("genotypes.snmfProject")
To remove the project, use:
remove.snmfProject("genotypes.snmfProject")
[1] "*************************************"
[1] "* sNMF K = 5 repetition 8 *"
[1] "*************************************"
summary of the options:
-n (number of individuals) 50
-L (number of loci) 400
-K (number of ancestral pops) 5
-x (input file) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/masked/genotypes_I.geno
-q (individual admixture file) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K5/run8/genotypes_r8.5.Q
-g (ancestral frequencies file) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K5/run8/genotypes_r8.5.G
-i (number max of iterations) 200
-a (regularization parameter) 10
-s (seed random init) 1947026275
-e (tolerance error) 1E-05
-p (number of processes) 1
- diploid
Read genotype file C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/masked/genotypes_I.geno: OK.
Main algorithm:
[ ]
[==================================]
Number of iterations: 91
Least-square error: 5259.789772
Write individual ancestry coefficient file C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K5/run8/genotypes_r8.5.Q: OK.
Write ancestral allele frequency coefficient file C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K5/run8/genotypes_r8.5.G: OK.
[1] "*************************************"
[1] "* cross-entropy estimation *"
[1] "*************************************"
summary of the options:
-n (number of individuals) 50
-L (number of loci) 400
-K (number of ancestral pops) 5
-x (genotype file) C:\Users\biocbuild\bbs-3.5-bioc\meat\LEA.Rcheck\examples_i386\genotypes.geno
-q (individual admixture) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K5/run8/genotypes_r8.5.Q
-g (ancestral frequencies) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K5/run8/genotypes_r8.5.G
-i (with masked genotypes) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/masked/genotypes_I.geno
- diploid
Cross-Entropy (all data): 0.433483
Cross-Entropy (masked data): 0.60242
The project is saved into :
genotypes.snmfProject
To load the project, use:
project = load.snmfProject("genotypes.snmfProject")
To remove the project, use:
remove.snmfProject("genotypes.snmfProject")
[1] "*************************************"
[1] "* sNMF K = 6 repetition 8 *"
[1] "*************************************"
summary of the options:
-n (number of individuals) 50
-L (number of loci) 400
-K (number of ancestral pops) 6
-x (input file) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/masked/genotypes_I.geno
-q (individual admixture file) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K6/run8/genotypes_r8.6.Q
-g (ancestral frequencies file) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K6/run8/genotypes_r8.6.G
-i (number max of iterations) 200
-a (regularization parameter) 10
-s (seed random init) 1947026275
-e (tolerance error) 1E-05
-p (number of processes) 1
- diploid
Read genotype file C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/masked/genotypes_I.geno: OK.
Main algorithm:
[ ]
[===================]
Number of iterations: 52
Least-square error: 5091.031350
Write individual ancestry coefficient file C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K6/run8/genotypes_r8.6.Q: OK.
Write ancestral allele frequency coefficient file C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K6/run8/genotypes_r8.6.G: OK.
[1] "*************************************"
[1] "* cross-entropy estimation *"
[1] "*************************************"
summary of the options:
-n (number of individuals) 50
-L (number of loci) 400
-K (number of ancestral pops) 6
-x (genotype file) C:\Users\biocbuild\bbs-3.5-bioc\meat\LEA.Rcheck\examples_i386\genotypes.geno
-q (individual admixture) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K6/run8/genotypes_r8.6.Q
-g (ancestral frequencies) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K6/run8/genotypes_r8.6.G
-i (with masked genotypes) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/masked/genotypes_I.geno
- diploid
Cross-Entropy (all data): 0.418418
Cross-Entropy (masked data): 0.629
The project is saved into :
genotypes.snmfProject
To load the project, use:
project = load.snmfProject("genotypes.snmfProject")
To remove the project, use:
remove.snmfProject("genotypes.snmfProject")
[1] "*************************************"
[1] "* sNMF K = 7 repetition 8 *"
[1] "*************************************"
summary of the options:
-n (number of individuals) 50
-L (number of loci) 400
-K (number of ancestral pops) 7
-x (input file) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/masked/genotypes_I.geno
-q (individual admixture file) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K7/run8/genotypes_r8.7.Q
-g (ancestral frequencies file) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K7/run8/genotypes_r8.7.G
-i (number max of iterations) 200
-a (regularization parameter) 10
-s (seed random init) 1947026275
-e (tolerance error) 1E-05
-p (number of processes) 1
- diploid
Read genotype file C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/masked/genotypes_I.geno: OK.
Main algorithm:
[ ]
[==========]
Number of iterations: 28
Least-square error: 4922.175791
Write individual ancestry coefficient file C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K7/run8/genotypes_r8.7.Q: OK.
Write ancestral allele frequency coefficient file C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K7/run8/genotypes_r8.7.G: OK.
[1] "*************************************"
[1] "* cross-entropy estimation *"
[1] "*************************************"
summary of the options:
-n (number of individuals) 50
-L (number of loci) 400
-K (number of ancestral pops) 7
-x (genotype file) C:\Users\biocbuild\bbs-3.5-bioc\meat\LEA.Rcheck\examples_i386\genotypes.geno
-q (individual admixture) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K7/run8/genotypes_r8.7.Q
-g (ancestral frequencies) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K7/run8/genotypes_r8.7.G
-i (with masked genotypes) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/masked/genotypes_I.geno
- diploid
Cross-Entropy (all data): 0.40367
Cross-Entropy (masked data): 0.658315
The project is saved into :
genotypes.snmfProject
To load the project, use:
project = load.snmfProject("genotypes.snmfProject")
To remove the project, use:
remove.snmfProject("genotypes.snmfProject")
[1] "*************************************"
[1] "* sNMF K = 8 repetition 8 *"
[1] "*************************************"
summary of the options:
-n (number of individuals) 50
-L (number of loci) 400
-K (number of ancestral pops) 8
-x (input file) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/masked/genotypes_I.geno
-q (individual admixture file) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K8/run8/genotypes_r8.8.Q
-g (ancestral frequencies file) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K8/run8/genotypes_r8.8.G
-i (number max of iterations) 200
-a (regularization parameter) 10
-s (seed random init) 1947026275
-e (tolerance error) 1E-05
-p (number of processes) 1
- diploid
Read genotype file C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/masked/genotypes_I.geno: OK.
Main algorithm:
[ ]
[=====================]
Number of iterations: 56
Least-square error: 4786.050511
Write individual ancestry coefficient file C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K8/run8/genotypes_r8.8.Q: OK.
Write ancestral allele frequency coefficient file C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K8/run8/genotypes_r8.8.G: OK.
[1] "*************************************"
[1] "* cross-entropy estimation *"
[1] "*************************************"
summary of the options:
-n (number of individuals) 50
-L (number of loci) 400
-K (number of ancestral pops) 8
-x (genotype file) C:\Users\biocbuild\bbs-3.5-bioc\meat\LEA.Rcheck\examples_i386\genotypes.geno
-q (individual admixture) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K8/run8/genotypes_r8.8.Q
-g (ancestral frequencies) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K8/run8/genotypes_r8.8.G
-i (with masked genotypes) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/masked/genotypes_I.geno
- diploid
Cross-Entropy (all data): 0.389176
Cross-Entropy (masked data): 0.688916
The project is saved into :
genotypes.snmfProject
To load the project, use:
project = load.snmfProject("genotypes.snmfProject")
To remove the project, use:
remove.snmfProject("genotypes.snmfProject")
[1] "*************************************"
[1] "* sNMF K = 9 repetition 8 *"
[1] "*************************************"
summary of the options:
-n (number of individuals) 50
-L (number of loci) 400
-K (number of ancestral pops) 9
-x (input file) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/masked/genotypes_I.geno
-q (individual admixture file) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K9/run8/genotypes_r8.9.Q
-g (ancestral frequencies file) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K9/run8/genotypes_r8.9.G
-i (number max of iterations) 200
-a (regularization parameter) 10
-s (seed random init) 1947026275
-e (tolerance error) 1E-05
-p (number of processes) 1
- diploid
Read genotype file C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/masked/genotypes_I.geno: OK.
Main algorithm:
[ ]
[=============]
Number of iterations: 35
Least-square error: 4693.101339
Write individual ancestry coefficient file C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K9/run8/genotypes_r8.9.Q: OK.
Write ancestral allele frequency coefficient file C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K9/run8/genotypes_r8.9.G: OK.
[1] "*************************************"
[1] "* cross-entropy estimation *"
[1] "*************************************"
summary of the options:
-n (number of individuals) 50
-L (number of loci) 400
-K (number of ancestral pops) 9
-x (genotype file) C:\Users\biocbuild\bbs-3.5-bioc\meat\LEA.Rcheck\examples_i386\genotypes.geno
-q (individual admixture) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K9/run8/genotypes_r8.9.Q
-g (ancestral frequencies) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K9/run8/genotypes_r8.9.G
-i (with masked genotypes) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/masked/genotypes_I.geno
- diploid
Cross-Entropy (all data): 0.381797
Cross-Entropy (masked data): 0.748445
The project is saved into :
genotypes.snmfProject
To load the project, use:
project = load.snmfProject("genotypes.snmfProject")
To remove the project, use:
remove.snmfProject("genotypes.snmfProject")
[1] "*************************************"
[1] "* sNMF K = 10 repetition 8 *"
[1] "*************************************"
summary of the options:
-n (number of individuals) 50
-L (number of loci) 400
-K (number of ancestral pops) 10
-x (input file) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/masked/genotypes_I.geno
-q (individual admixture file) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K10/run8/genotypes_r8.10.Q
-g (ancestral frequencies file) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K10/run8/genotypes_r8.10.G
-i (number max of iterations) 200
-a (regularization parameter) 10
-s (seed random init) 1947026275
-e (tolerance error) 1E-05
-p (number of processes) 1
- diploid
Read genotype file C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/masked/genotypes_I.geno: OK.
Main algorithm:
[ ]
[===============================]
Number of iterations: 84
Least-square error: 4496.760556
Write individual ancestry coefficient file C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K10/run8/genotypes_r8.10.Q: OK.
Write ancestral allele frequency coefficient file C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K10/run8/genotypes_r8.10.G: OK.
[1] "*************************************"
[1] "* cross-entropy estimation *"
[1] "*************************************"
summary of the options:
-n (number of individuals) 50
-L (number of loci) 400
-K (number of ancestral pops) 10
-x (genotype file) C:\Users\biocbuild\bbs-3.5-bioc\meat\LEA.Rcheck\examples_i386\genotypes.geno
-q (individual admixture) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K10/run8/genotypes_r8.10.Q
-g (ancestral frequencies) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K10/run8/genotypes_r8.10.G
-i (with masked genotypes) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/masked/genotypes_I.geno
- diploid
Cross-Entropy (all data): 0.363105
Cross-Entropy (masked data): 0.749189
The project is saved into :
genotypes.snmfProject
To load the project, use:
project = load.snmfProject("genotypes.snmfProject")
To remove the project, use:
remove.snmfProject("genotypes.snmfProject")
[1] 942839743
[1] "*************************************"
[1] "* create.dataset *"
[1] "*************************************"
summary of the options:
-n (number of individuals) 50
-L (number of loci) 400
-s (seed random init) 942839743
-r (percentage of masked data) 0.05
-x (genotype file in .geno format) C:\Users\biocbuild\bbs-3.5-bioc\meat\LEA.Rcheck\examples_i386\genotypes.geno
-o (output file in .geno format) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/masked/genotypes_I.geno
Write genotype file with masked data, C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/masked/genotypes_I.geno: OK.
[1] "*************************************"
[1] "* sNMF K = 1 repetition 9 *"
[1] "*************************************"
summary of the options:
-n (number of individuals) 50
-L (number of loci) 400
-K (number of ancestral pops) 1
-x (input file) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/masked/genotypes_I.geno
-q (individual admixture file) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K1/run9/genotypes_r9.1.Q
-g (ancestral frequencies file) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K1/run9/genotypes_r9.1.G
-i (number max of iterations) 200
-a (regularization parameter) 10
-s (seed random init) 942839743
-e (tolerance error) 1E-05
-p (number of processes) 1
- diploid
Read genotype file C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/masked/genotypes_I.geno: OK.
Main algorithm:
Least-square error: 6659.240084
Write individual ancestry coefficient file C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K1/run9/genotypes_r9.1.Q: OK.
Write ancestral allele frequency coefficient file C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K1/run9/genotypes_r9.1.G: OK.
[1] "*************************************"
[1] "* cross-entropy estimation *"
[1] "*************************************"
summary of the options:
-n (number of individuals) 50
-L (number of loci) 400
-K (number of ancestral pops) 1
-x (genotype file) C:\Users\biocbuild\bbs-3.5-bioc\meat\LEA.Rcheck\examples_i386\genotypes.geno
-q (individual admixture) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K1/run9/genotypes_r9.1.Q
-g (ancestral frequencies) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K1/run9/genotypes_r9.1.G
-i (with masked genotypes) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/masked/genotypes_I.geno
- diploid
Cross-Entropy (all data): 0.575173
Cross-Entropy (masked data): 0.692632
The project is saved into :
genotypes.snmfProject
To load the project, use:
project = load.snmfProject("genotypes.snmfProject")
To remove the project, use:
remove.snmfProject("genotypes.snmfProject")
[1] "*************************************"
[1] "* sNMF K = 2 repetition 9 *"
[1] "*************************************"
summary of the options:
-n (number of individuals) 50
-L (number of loci) 400
-K (number of ancestral pops) 2
-x (input file) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/masked/genotypes_I.geno
-q (individual admixture file) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K2/run9/genotypes_r9.2.Q
-g (ancestral frequencies file) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K2/run9/genotypes_r9.2.G
-i (number max of iterations) 200
-a (regularization parameter) 10
-s (seed random init) 942839743
-e (tolerance error) 1E-05
-p (number of processes) 1
- diploid
Read genotype file C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/masked/genotypes_I.geno: OK.
Main algorithm:
[ ]
[=============]
Number of iterations: 34
Least-square error: 6135.989143
Write individual ancestry coefficient file C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K2/run9/genotypes_r9.2.Q: OK.
Write ancestral allele frequency coefficient file C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K2/run9/genotypes_r9.2.G: OK.
[1] "*************************************"
[1] "* cross-entropy estimation *"
[1] "*************************************"
summary of the options:
-n (number of individuals) 50
-L (number of loci) 400
-K (number of ancestral pops) 2
-x (genotype file) C:\Users\biocbuild\bbs-3.5-bioc\meat\LEA.Rcheck\examples_i386\genotypes.geno
-q (individual admixture) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K2/run9/genotypes_r9.2.Q
-g (ancestral frequencies) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K2/run9/genotypes_r9.2.G
-i (with masked genotypes) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/masked/genotypes_I.geno
- diploid
Cross-Entropy (all data): 0.518124
Cross-Entropy (masked data): 0.656592
The project is saved into :
genotypes.snmfProject
To load the project, use:
project = load.snmfProject("genotypes.snmfProject")
To remove the project, use:
remove.snmfProject("genotypes.snmfProject")
[1] "*************************************"
[1] "* sNMF K = 3 repetition 9 *"
[1] "*************************************"
summary of the options:
-n (number of individuals) 50
-L (number of loci) 400
-K (number of ancestral pops) 3
-x (input file) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/masked/genotypes_I.geno
-q (individual admixture file) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K3/run9/genotypes_r9.3.Q
-g (ancestral frequencies file) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K3/run9/genotypes_r9.3.G
-i (number max of iterations) 200
-a (regularization parameter) 10
-s (seed random init) 942839743
-e (tolerance error) 1E-05
-p (number of processes) 1
- diploid
Read genotype file C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/masked/genotypes_I.geno: OK.
Main algorithm:
[ ]
[========================]
Number of iterations: 65
Least-square error: 5686.977480
Write individual ancestry coefficient file C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K3/run9/genotypes_r9.3.Q: OK.
Write ancestral allele frequency coefficient file C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K3/run9/genotypes_r9.3.G: OK.
[1] "*************************************"
[1] "* cross-entropy estimation *"
[1] "*************************************"
summary of the options:
-n (number of individuals) 50
-L (number of loci) 400
-K (number of ancestral pops) 3
-x (genotype file) C:\Users\biocbuild\bbs-3.5-bioc\meat\LEA.Rcheck\examples_i386\genotypes.geno
-q (individual admixture) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K3/run9/genotypes_r9.3.Q
-g (ancestral frequencies) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K3/run9/genotypes_r9.3.G
-i (with masked genotypes) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/masked/genotypes_I.geno
- diploid
Cross-Entropy (all data): 0.475121
Cross-Entropy (masked data): 0.649742
The project is saved into :
genotypes.snmfProject
To load the project, use:
project = load.snmfProject("genotypes.snmfProject")
To remove the project, use:
remove.snmfProject("genotypes.snmfProject")
[1] "*************************************"
[1] "* sNMF K = 4 repetition 9 *"
[1] "*************************************"
summary of the options:
-n (number of individuals) 50
-L (number of loci) 400
-K (number of ancestral pops) 4
-x (input file) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/masked/genotypes_I.geno
-q (individual admixture file) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K4/run9/genotypes_r9.4.Q
-g (ancestral frequencies file) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K4/run9/genotypes_r9.4.G
-i (number max of iterations) 200
-a (regularization parameter) 10
-s (seed random init) 942839743
-e (tolerance error) 1E-05
-p (number of processes) 1
- diploid
Read genotype file C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/masked/genotypes_I.geno: OK.
Main algorithm:
[ ]
[=======================]
Number of iterations: 62
Least-square error: 5441.424379
Write individual ancestry coefficient file C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K4/run9/genotypes_r9.4.Q: OK.
Write ancestral allele frequency coefficient file C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K4/run9/genotypes_r9.4.G: OK.
[1] "*************************************"
[1] "* cross-entropy estimation *"
[1] "*************************************"
summary of the options:
-n (number of individuals) 50
-L (number of loci) 400
-K (number of ancestral pops) 4
-x (genotype file) C:\Users\biocbuild\bbs-3.5-bioc\meat\LEA.Rcheck\examples_i386\genotypes.geno
-q (individual admixture) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K4/run9/genotypes_r9.4.Q
-g (ancestral frequencies) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K4/run9/genotypes_r9.4.G
-i (with masked genotypes) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/masked/genotypes_I.geno
- diploid
Cross-Entropy (all data): 0.450344
Cross-Entropy (masked data): 0.624977
The project is saved into :
genotypes.snmfProject
To load the project, use:
project = load.snmfProject("genotypes.snmfProject")
To remove the project, use:
remove.snmfProject("genotypes.snmfProject")
[1] "*************************************"
[1] "* sNMF K = 5 repetition 9 *"
[1] "*************************************"
summary of the options:
-n (number of individuals) 50
-L (number of loci) 400
-K (number of ancestral pops) 5
-x (input file) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/masked/genotypes_I.geno
-q (individual admixture file) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K5/run9/genotypes_r9.5.Q
-g (ancestral frequencies file) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K5/run9/genotypes_r9.5.G
-i (number max of iterations) 200
-a (regularization parameter) 10
-s (seed random init) 942839743
-e (tolerance error) 1E-05
-p (number of processes) 1
- diploid
Read genotype file C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/masked/genotypes_I.geno: OK.
Main algorithm:
[ ]
[======================]
Number of iterations: 59
Least-square error: 5260.836412
Write individual ancestry coefficient file C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K5/run9/genotypes_r9.5.Q: OK.
Write ancestral allele frequency coefficient file C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K5/run9/genotypes_r9.5.G: OK.
[1] "*************************************"
[1] "* cross-entropy estimation *"
[1] "*************************************"
summary of the options:
-n (number of individuals) 50
-L (number of loci) 400
-K (number of ancestral pops) 5
-x (genotype file) C:\Users\biocbuild\bbs-3.5-bioc\meat\LEA.Rcheck\examples_i386\genotypes.geno
-q (individual admixture) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K5/run9/genotypes_r9.5.Q
-g (ancestral frequencies) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K5/run9/genotypes_r9.5.G
-i (with masked genotypes) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/masked/genotypes_I.geno
- diploid
Cross-Entropy (all data): 0.433057
Cross-Entropy (masked data): 0.62932
The project is saved into :
genotypes.snmfProject
To load the project, use:
project = load.snmfProject("genotypes.snmfProject")
To remove the project, use:
remove.snmfProject("genotypes.snmfProject")
[1] "*************************************"
[1] "* sNMF K = 6 repetition 9 *"
[1] "*************************************"
summary of the options:
-n (number of individuals) 50
-L (number of loci) 400
-K (number of ancestral pops) 6
-x (input file) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/masked/genotypes_I.geno
-q (individual admixture file) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K6/run9/genotypes_r9.6.Q
-g (ancestral frequencies file) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K6/run9/genotypes_r9.6.G
-i (number max of iterations) 200
-a (regularization parameter) 10
-s (seed random init) 942839743
-e (tolerance error) 1E-05
-p (number of processes) 1
- diploid
Read genotype file C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/masked/genotypes_I.geno: OK.
Main algorithm:
[ ]
[===========================]
Number of iterations: 72
Least-square error: 5049.782681
Write individual ancestry coefficient file C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K6/run9/genotypes_r9.6.Q: OK.
Write ancestral allele frequency coefficient file C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K6/run9/genotypes_r9.6.G: OK.
[1] "*************************************"
[1] "* cross-entropy estimation *"
[1] "*************************************"
summary of the options:
-n (number of individuals) 50
-L (number of loci) 400
-K (number of ancestral pops) 6
-x (genotype file) C:\Users\biocbuild\bbs-3.5-bioc\meat\LEA.Rcheck\examples_i386\genotypes.geno
-q (individual admixture) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K6/run9/genotypes_r9.6.Q
-g (ancestral frequencies) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K6/run9/genotypes_r9.6.G
-i (with masked genotypes) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/masked/genotypes_I.geno
- diploid
Cross-Entropy (all data): 0.415211
Cross-Entropy (masked data): 0.6899
The project is saved into :
genotypes.snmfProject
To load the project, use:
project = load.snmfProject("genotypes.snmfProject")
To remove the project, use:
remove.snmfProject("genotypes.snmfProject")
[1] "*************************************"
[1] "* sNMF K = 7 repetition 9 *"
[1] "*************************************"
summary of the options:
-n (number of individuals) 50
-L (number of loci) 400
-K (number of ancestral pops) 7
-x (input file) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/masked/genotypes_I.geno
-q (individual admixture file) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K7/run9/genotypes_r9.7.Q
-g (ancestral frequencies file) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K7/run9/genotypes_r9.7.G
-i (number max of iterations) 200
-a (regularization parameter) 10
-s (seed random init) 942839743
-e (tolerance error) 1E-05
-p (number of processes) 1
- diploid
Read genotype file C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/masked/genotypes_I.geno: OK.
Main algorithm:
[ ]
[===========================================================================]
Number of iterations: 200
Least-square error: 4926.490009
Write individual ancestry coefficient file C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K7/run9/genotypes_r9.7.Q: OK.
Write ancestral allele frequency coefficient file C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K7/run9/genotypes_r9.7.G: OK.
[1] "*************************************"
[1] "* cross-entropy estimation *"
[1] "*************************************"
summary of the options:
-n (number of individuals) 50
-L (number of loci) 400
-K (number of ancestral pops) 7
-x (genotype file) C:\Users\biocbuild\bbs-3.5-bioc\meat\LEA.Rcheck\examples_i386\genotypes.geno
-q (individual admixture) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K7/run9/genotypes_r9.7.Q
-g (ancestral frequencies) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K7/run9/genotypes_r9.7.G
-i (with masked genotypes) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/masked/genotypes_I.geno
- diploid
Cross-Entropy (all data): 0.40282
Cross-Entropy (masked data): 0.704344
The project is saved into :
genotypes.snmfProject
To load the project, use:
project = load.snmfProject("genotypes.snmfProject")
To remove the project, use:
remove.snmfProject("genotypes.snmfProject")
[1] "*************************************"
[1] "* sNMF K = 8 repetition 9 *"
[1] "*************************************"
summary of the options:
-n (number of individuals) 50
-L (number of loci) 400
-K (number of ancestral pops) 8
-x (input file) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/masked/genotypes_I.geno
-q (individual admixture file) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K8/run9/genotypes_r9.8.Q
-g (ancestral frequencies file) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K8/run9/genotypes_r9.8.G
-i (number max of iterations) 200
-a (regularization parameter) 10
-s (seed random init) 942839743
-e (tolerance error) 1E-05
-p (number of processes) 1
- diploid
Read genotype file C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/masked/genotypes_I.geno: OK.
Main algorithm:
[ ]
[===================]
Number of iterations: 51
Least-square error: 4796.708174
Write individual ancestry coefficient file C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K8/run9/genotypes_r9.8.Q: OK.
Write ancestral allele frequency coefficient file C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K8/run9/genotypes_r9.8.G: OK.
[1] "*************************************"
[1] "* cross-entropy estimation *"
[1] "*************************************"
summary of the options:
-n (number of individuals) 50
-L (number of loci) 400
-K (number of ancestral pops) 8
-x (genotype file) C:\Users\biocbuild\bbs-3.5-bioc\meat\LEA.Rcheck\examples_i386\genotypes.geno
-q (individual admixture) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K8/run9/genotypes_r9.8.Q
-g (ancestral frequencies) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K8/run9/genotypes_r9.8.G
-i (with masked genotypes) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/masked/genotypes_I.geno
- diploid
Cross-Entropy (all data): 0.390742
Cross-Entropy (masked data): 0.706284
The project is saved into :
genotypes.snmfProject
To load the project, use:
project = load.snmfProject("genotypes.snmfProject")
To remove the project, use:
remove.snmfProject("genotypes.snmfProject")
[1] "*************************************"
[1] "* sNMF K = 9 repetition 9 *"
[1] "*************************************"
summary of the options:
-n (number of individuals) 50
-L (number of loci) 400
-K (number of ancestral pops) 9
-x (input file) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/masked/genotypes_I.geno
-q (individual admixture file) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K9/run9/genotypes_r9.9.Q
-g (ancestral frequencies file) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K9/run9/genotypes_r9.9.G
-i (number max of iterations) 200
-a (regularization parameter) 10
-s (seed random init) 942839743
-e (tolerance error) 1E-05
-p (number of processes) 1
- diploid
Read genotype file C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/masked/genotypes_I.geno: OK.
Main algorithm:
[ ]
[=======================================]
Number of iterations: 103
Least-square error: 4675.171296
Write individual ancestry coefficient file C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K9/run9/genotypes_r9.9.Q: OK.
Write ancestral allele frequency coefficient file C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K9/run9/genotypes_r9.9.G: OK.
[1] "*************************************"
[1] "* cross-entropy estimation *"
[1] "*************************************"
summary of the options:
-n (number of individuals) 50
-L (number of loci) 400
-K (number of ancestral pops) 9
-x (genotype file) C:\Users\biocbuild\bbs-3.5-bioc\meat\LEA.Rcheck\examples_i386\genotypes.geno
-q (individual admixture) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K9/run9/genotypes_r9.9.Q
-g (ancestral frequencies) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K9/run9/genotypes_r9.9.G
-i (with masked genotypes) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/masked/genotypes_I.geno
- diploid
Cross-Entropy (all data): 0.380874
Cross-Entropy (masked data): 0.804861
The project is saved into :
genotypes.snmfProject
To load the project, use:
project = load.snmfProject("genotypes.snmfProject")
To remove the project, use:
remove.snmfProject("genotypes.snmfProject")
[1] "*************************************"
[1] "* sNMF K = 10 repetition 9 *"
[1] "*************************************"
summary of the options:
-n (number of individuals) 50
-L (number of loci) 400
-K (number of ancestral pops) 10
-x (input file) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/masked/genotypes_I.geno
-q (individual admixture file) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K10/run9/genotypes_r9.10.Q
-g (ancestral frequencies file) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K10/run9/genotypes_r9.10.G
-i (number max of iterations) 200
-a (regularization parameter) 10
-s (seed random init) 942839743
-e (tolerance error) 1E-05
-p (number of processes) 1
- diploid
Read genotype file C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/masked/genotypes_I.geno: OK.
Main algorithm:
[ ]
[==================================================================]
Number of iterations: 176
Least-square error: 4508.846037
Write individual ancestry coefficient file C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K10/run9/genotypes_r9.10.Q: OK.
Write ancestral allele frequency coefficient file C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K10/run9/genotypes_r9.10.G: OK.
[1] "*************************************"
[1] "* cross-entropy estimation *"
[1] "*************************************"
summary of the options:
-n (number of individuals) 50
-L (number of loci) 400
-K (number of ancestral pops) 10
-x (genotype file) C:\Users\biocbuild\bbs-3.5-bioc\meat\LEA.Rcheck\examples_i386\genotypes.geno
-q (individual admixture) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K10/run9/genotypes_r9.10.Q
-g (ancestral frequencies) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K10/run9/genotypes_r9.10.G
-i (with masked genotypes) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/masked/genotypes_I.geno
- diploid
Cross-Entropy (all data): 0.363169
Cross-Entropy (masked data): 0.777179
The project is saved into :
genotypes.snmfProject
To load the project, use:
project = load.snmfProject("genotypes.snmfProject")
To remove the project, use:
remove.snmfProject("genotypes.snmfProject")
[1] 1191190572
[1] "*************************************"
[1] "* create.dataset *"
[1] "*************************************"
summary of the options:
-n (number of individuals) 50
-L (number of loci) 400
-s (seed random init) 1191190572
-r (percentage of masked data) 0.05
-x (genotype file in .geno format) C:\Users\biocbuild\bbs-3.5-bioc\meat\LEA.Rcheck\examples_i386\genotypes.geno
-o (output file in .geno format) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/masked/genotypes_I.geno
Write genotype file with masked data, C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/masked/genotypes_I.geno: OK.
[1] "*************************************"
[1] "* sNMF K = 1 repetition 10 *"
[1] "*************************************"
summary of the options:
-n (number of individuals) 50
-L (number of loci) 400
-K (number of ancestral pops) 1
-x (input file) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/masked/genotypes_I.geno
-q (individual admixture file) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K1/run10/genotypes_r10.1.Q
-g (ancestral frequencies file) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K1/run10/genotypes_r10.1.G
-i (number max of iterations) 200
-a (regularization parameter) 10
-s (seed random init) 1191190572
-e (tolerance error) 1E-05
-p (number of processes) 1
- diploid
Read genotype file C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/masked/genotypes_I.geno: OK.
Main algorithm:
Least-square error: 6666.280082
Write individual ancestry coefficient file C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K1/run10/genotypes_r10.1.Q: OK.
Write ancestral allele frequency coefficient file C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K1/run10/genotypes_r10.1.G: OK.
[1] "*************************************"
[1] "* cross-entropy estimation *"
[1] "*************************************"
summary of the options:
-n (number of individuals) 50
-L (number of loci) 400
-K (number of ancestral pops) 1
-x (genotype file) C:\Users\biocbuild\bbs-3.5-bioc\meat\LEA.Rcheck\examples_i386\genotypes.geno
-q (individual admixture) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K1/run10/genotypes_r10.1.Q
-g (ancestral frequencies) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K1/run10/genotypes_r10.1.G
-i (with masked genotypes) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/masked/genotypes_I.geno
- diploid
Cross-Entropy (all data): 0.576346
Cross-Entropy (masked data): 0.651475
The project is saved into :
genotypes.snmfProject
To load the project, use:
project = load.snmfProject("genotypes.snmfProject")
To remove the project, use:
remove.snmfProject("genotypes.snmfProject")
[1] "*************************************"
[1] "* sNMF K = 2 repetition 10 *"
[1] "*************************************"
summary of the options:
-n (number of individuals) 50
-L (number of loci) 400
-K (number of ancestral pops) 2
-x (input file) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/masked/genotypes_I.geno
-q (individual admixture file) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K2/run10/genotypes_r10.2.Q
-g (ancestral frequencies file) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K2/run10/genotypes_r10.2.G
-i (number max of iterations) 200
-a (regularization parameter) 10
-s (seed random init) 1191190572
-e (tolerance error) 1E-05
-p (number of processes) 1
- diploid
Read genotype file C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/masked/genotypes_I.geno: OK.
Main algorithm:
[ ]
[==============]
Number of iterations: 38
Least-square error: 6089.834039
Write individual ancestry coefficient file C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K2/run10/genotypes_r10.2.Q: OK.
Write ancestral allele frequency coefficient file C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K2/run10/genotypes_r10.2.G: OK.
[1] "*************************************"
[1] "* cross-entropy estimation *"
[1] "*************************************"
summary of the options:
-n (number of individuals) 50
-L (number of loci) 400
-K (number of ancestral pops) 2
-x (genotype file) C:\Users\biocbuild\bbs-3.5-bioc\meat\LEA.Rcheck\examples_i386\genotypes.geno
-q (individual admixture) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K2/run10/genotypes_r10.2.Q
-g (ancestral frequencies) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K2/run10/genotypes_r10.2.G
-i (with masked genotypes) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/masked/genotypes_I.geno
- diploid
Cross-Entropy (all data): 0.517382
Cross-Entropy (masked data): 0.639851
The project is saved into :
genotypes.snmfProject
To load the project, use:
project = load.snmfProject("genotypes.snmfProject")
To remove the project, use:
remove.snmfProject("genotypes.snmfProject")
[1] "*************************************"
[1] "* sNMF K = 3 repetition 10 *"
[1] "*************************************"
summary of the options:
-n (number of individuals) 50
-L (number of loci) 400
-K (number of ancestral pops) 3
-x (input file) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/masked/genotypes_I.geno
-q (individual admixture file) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K3/run10/genotypes_r10.3.Q
-g (ancestral frequencies file) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K3/run10/genotypes_r10.3.G
-i (number max of iterations) 200
-a (regularization parameter) 10
-s (seed random init) 1191190572
-e (tolerance error) 1E-05
-p (number of processes) 1
- diploid
Read genotype file C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/masked/genotypes_I.geno: OK.
Main algorithm:
[ ]
[============================]
Number of iterations: 76
Least-square error: 5683.930032
Write individual ancestry coefficient file C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K3/run10/genotypes_r10.3.Q: OK.
Write ancestral allele frequency coefficient file C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K3/run10/genotypes_r10.3.G: OK.
[1] "*************************************"
[1] "* cross-entropy estimation *"
[1] "*************************************"
summary of the options:
-n (number of individuals) 50
-L (number of loci) 400
-K (number of ancestral pops) 3
-x (genotype file) C:\Users\biocbuild\bbs-3.5-bioc\meat\LEA.Rcheck\examples_i386\genotypes.geno
-q (individual admixture) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K3/run10/genotypes_r10.3.Q
-g (ancestral frequencies) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K3/run10/genotypes_r10.3.G
-i (with masked genotypes) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/masked/genotypes_I.geno
- diploid
Cross-Entropy (all data): 0.476297
Cross-Entropy (masked data): 0.585068
The project is saved into :
genotypes.snmfProject
To load the project, use:
project = load.snmfProject("genotypes.snmfProject")
To remove the project, use:
remove.snmfProject("genotypes.snmfProject")
[1] "*************************************"
[1] "* sNMF K = 4 repetition 10 *"
[1] "*************************************"
summary of the options:
-n (number of individuals) 50
-L (number of loci) 400
-K (number of ancestral pops) 4
-x (input file) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/masked/genotypes_I.geno
-q (individual admixture file) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K4/run10/genotypes_r10.4.Q
-g (ancestral frequencies file) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K4/run10/genotypes_r10.4.G
-i (number max of iterations) 200
-a (regularization parameter) 10
-s (seed random init) 1191190572
-e (tolerance error) 1E-05
-p (number of processes) 1
- diploid
Read genotype file C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/masked/genotypes_I.geno: OK.
Main algorithm:
[ ]
[=======================]
Number of iterations: 62
Least-square error: 5456.754007
Write individual ancestry coefficient file C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K4/run10/genotypes_r10.4.Q: OK.
Write ancestral allele frequency coefficient file C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K4/run10/genotypes_r10.4.G: OK.
[1] "*************************************"
[1] "* cross-entropy estimation *"
[1] "*************************************"
summary of the options:
-n (number of individuals) 50
-L (number of loci) 400
-K (number of ancestral pops) 4
-x (genotype file) C:\Users\biocbuild\bbs-3.5-bioc\meat\LEA.Rcheck\examples_i386\genotypes.geno
-q (individual admixture) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K4/run10/genotypes_r10.4.Q
-g (ancestral frequencies) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K4/run10/genotypes_r10.4.G
-i (with masked genotypes) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/masked/genotypes_I.geno
- diploid
Cross-Entropy (all data): 0.450813
Cross-Entropy (masked data): 0.597699
The project is saved into :
genotypes.snmfProject
To load the project, use:
project = load.snmfProject("genotypes.snmfProject")
To remove the project, use:
remove.snmfProject("genotypes.snmfProject")
[1] "*************************************"
[1] "* sNMF K = 5 repetition 10 *"
[1] "*************************************"
summary of the options:
-n (number of individuals) 50
-L (number of loci) 400
-K (number of ancestral pops) 5
-x (input file) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/masked/genotypes_I.geno
-q (individual admixture file) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K5/run10/genotypes_r10.5.Q
-g (ancestral frequencies file) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K5/run10/genotypes_r10.5.G
-i (number max of iterations) 200
-a (regularization parameter) 10
-s (seed random init) 1191190572
-e (tolerance error) 1E-05
-p (number of processes) 1
- diploid
Read genotype file C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/masked/genotypes_I.geno: OK.
Main algorithm:
[ ]
[========================]
Number of iterations: 65
Least-square error: 5253.022180
Write individual ancestry coefficient file C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K5/run10/genotypes_r10.5.Q: OK.
Write ancestral allele frequency coefficient file C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K5/run10/genotypes_r10.5.G: OK.
[1] "*************************************"
[1] "* cross-entropy estimation *"
[1] "*************************************"
summary of the options:
-n (number of individuals) 50
-L (number of loci) 400
-K (number of ancestral pops) 5
-x (genotype file) C:\Users\biocbuild\bbs-3.5-bioc\meat\LEA.Rcheck\examples_i386\genotypes.geno
-q (individual admixture) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K5/run10/genotypes_r10.5.Q
-g (ancestral frequencies) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K5/run10/genotypes_r10.5.G
-i (with masked genotypes) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/masked/genotypes_I.geno
- diploid
Cross-Entropy (all data): 0.432132
Cross-Entropy (masked data): 0.616705
The project is saved into :
genotypes.snmfProject
To load the project, use:
project = load.snmfProject("genotypes.snmfProject")
To remove the project, use:
remove.snmfProject("genotypes.snmfProject")
[1] "*************************************"
[1] "* sNMF K = 6 repetition 10 *"
[1] "*************************************"
summary of the options:
-n (number of individuals) 50
-L (number of loci) 400
-K (number of ancestral pops) 6
-x (input file) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/masked/genotypes_I.geno
-q (individual admixture file) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K6/run10/genotypes_r10.6.Q
-g (ancestral frequencies file) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K6/run10/genotypes_r10.6.G
-i (number max of iterations) 200
-a (regularization parameter) 10
-s (seed random init) 1191190572
-e (tolerance error) 1E-05
-p (number of processes) 1
- diploid
Read genotype file C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/masked/genotypes_I.geno: OK.
Main algorithm:
[ ]
[==========]
Number of iterations: 26
Least-square error: 5085.264366
Write individual ancestry coefficient file C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K6/run10/genotypes_r10.6.Q: OK.
Write ancestral allele frequency coefficient file C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K6/run10/genotypes_r10.6.G: OK.
[1] "*************************************"
[1] "* cross-entropy estimation *"
[1] "*************************************"
summary of the options:
-n (number of individuals) 50
-L (number of loci) 400
-K (number of ancestral pops) 6
-x (genotype file) C:\Users\biocbuild\bbs-3.5-bioc\meat\LEA.Rcheck\examples_i386\genotypes.geno
-q (individual admixture) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K6/run10/genotypes_r10.6.Q
-g (ancestral frequencies) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K6/run10/genotypes_r10.6.G
-i (with masked genotypes) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/masked/genotypes_I.geno
- diploid
Cross-Entropy (all data): 0.417964
Cross-Entropy (masked data): 0.637985
The project is saved into :
genotypes.snmfProject
To load the project, use:
project = load.snmfProject("genotypes.snmfProject")
To remove the project, use:
remove.snmfProject("genotypes.snmfProject")
[1] "*************************************"
[1] "* sNMF K = 7 repetition 10 *"
[1] "*************************************"
summary of the options:
-n (number of individuals) 50
-L (number of loci) 400
-K (number of ancestral pops) 7
-x (input file) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/masked/genotypes_I.geno
-q (individual admixture file) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K7/run10/genotypes_r10.7.Q
-g (ancestral frequencies file) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K7/run10/genotypes_r10.7.G
-i (number max of iterations) 200
-a (regularization parameter) 10
-s (seed random init) 1191190572
-e (tolerance error) 1E-05
-p (number of processes) 1
- diploid
Read genotype file C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/masked/genotypes_I.geno: OK.
Main algorithm:
[ ]
[================================]
Number of iterations: 86
Least-square error: 4975.002044
Write individual ancestry coefficient file C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K7/run10/genotypes_r10.7.Q: OK.
Write ancestral allele frequency coefficient file C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K7/run10/genotypes_r10.7.G: OK.
[1] "*************************************"
[1] "* cross-entropy estimation *"
[1] "*************************************"
summary of the options:
-n (number of individuals) 50
-L (number of loci) 400
-K (number of ancestral pops) 7
-x (genotype file) C:\Users\biocbuild\bbs-3.5-bioc\meat\LEA.Rcheck\examples_i386\genotypes.geno
-q (individual admixture) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K7/run10/genotypes_r10.7.Q
-g (ancestral frequencies) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K7/run10/genotypes_r10.7.G
-i (with masked genotypes) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/masked/genotypes_I.geno
- diploid
Cross-Entropy (all data): 0.404974
Cross-Entropy (masked data): 0.632853
The project is saved into :
genotypes.snmfProject
To load the project, use:
project = load.snmfProject("genotypes.snmfProject")
To remove the project, use:
remove.snmfProject("genotypes.snmfProject")
[1] "*************************************"
[1] "* sNMF K = 8 repetition 10 *"
[1] "*************************************"
summary of the options:
-n (number of individuals) 50
-L (number of loci) 400
-K (number of ancestral pops) 8
-x (input file) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/masked/genotypes_I.geno
-q (individual admixture file) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K8/run10/genotypes_r10.8.Q
-g (ancestral frequencies file) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K8/run10/genotypes_r10.8.G
-i (number max of iterations) 200
-a (regularization parameter) 10
-s (seed random init) 1191190572
-e (tolerance error) 1E-05
-p (number of processes) 1
- diploid
Read genotype file C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/masked/genotypes_I.geno: OK.
Main algorithm:
[ ]
[====================]
Number of iterations: 53
Least-square error: 4785.363791
Write individual ancestry coefficient file C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K8/run10/genotypes_r10.8.Q: OK.
Write ancestral allele frequency coefficient file C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K8/run10/genotypes_r10.8.G: OK.
[1] "*************************************"
[1] "* cross-entropy estimation *"
[1] "*************************************"
summary of the options:
-n (number of individuals) 50
-L (number of loci) 400
-K (number of ancestral pops) 8
-x (genotype file) C:\Users\biocbuild\bbs-3.5-bioc\meat\LEA.Rcheck\examples_i386\genotypes.geno
-q (individual admixture) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K8/run10/genotypes_r10.8.Q
-g (ancestral frequencies) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K8/run10/genotypes_r10.8.G
-i (with masked genotypes) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/masked/genotypes_I.geno
- diploid
Cross-Entropy (all data): 0.390876
Cross-Entropy (masked data): 0.71003
The project is saved into :
genotypes.snmfProject
To load the project, use:
project = load.snmfProject("genotypes.snmfProject")
To remove the project, use:
remove.snmfProject("genotypes.snmfProject")
[1] "*************************************"
[1] "* sNMF K = 9 repetition 10 *"
[1] "*************************************"
summary of the options:
-n (number of individuals) 50
-L (number of loci) 400
-K (number of ancestral pops) 9
-x (input file) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/masked/genotypes_I.geno
-q (individual admixture file) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K9/run10/genotypes_r10.9.Q
-g (ancestral frequencies file) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K9/run10/genotypes_r10.9.G
-i (number max of iterations) 200
-a (regularization parameter) 10
-s (seed random init) 1191190572
-e (tolerance error) 1E-05
-p (number of processes) 1
- diploid
Read genotype file C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/masked/genotypes_I.geno: OK.
Main algorithm:
[ ]
[====================================]
Number of iterations: 96
Least-square error: 4622.501901
Write individual ancestry coefficient file C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K9/run10/genotypes_r10.9.Q: OK.
Write ancestral allele frequency coefficient file C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K9/run10/genotypes_r10.9.G: OK.
[1] "*************************************"
[1] "* cross-entropy estimation *"
[1] "*************************************"
summary of the options:
-n (number of individuals) 50
-L (number of loci) 400
-K (number of ancestral pops) 9
-x (genotype file) C:\Users\biocbuild\bbs-3.5-bioc\meat\LEA.Rcheck\examples_i386\genotypes.geno
-q (individual admixture) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K9/run10/genotypes_r10.9.Q
-g (ancestral frequencies) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K9/run10/genotypes_r10.9.G
-i (with masked genotypes) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/masked/genotypes_I.geno
- diploid
Cross-Entropy (all data): 0.37593
Cross-Entropy (masked data): 0.760035
The project is saved into :
genotypes.snmfProject
To load the project, use:
project = load.snmfProject("genotypes.snmfProject")
To remove the project, use:
remove.snmfProject("genotypes.snmfProject")
[1] "*************************************"
[1] "* sNMF K = 10 repetition 10 *"
[1] "*************************************"
summary of the options:
-n (number of individuals) 50
-L (number of loci) 400
-K (number of ancestral pops) 10
-x (input file) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/masked/genotypes_I.geno
-q (individual admixture file) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K10/run10/genotypes_r10.10.Q
-g (ancestral frequencies file) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K10/run10/genotypes_r10.10.G
-i (number max of iterations) 200
-a (regularization parameter) 10
-s (seed random init) 1191190572
-e (tolerance error) 1E-05
-p (number of processes) 1
- diploid
Read genotype file C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/masked/genotypes_I.geno: OK.
Main algorithm:
[ ]
[=======================================================================]
Number of iterations: 190
Least-square error: 4495.298254
Write individual ancestry coefficient file C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K10/run10/genotypes_r10.10.Q: OK.
Write ancestral allele frequency coefficient file C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K10/run10/genotypes_r10.10.G: OK.
[1] "*************************************"
[1] "* cross-entropy estimation *"
[1] "*************************************"
summary of the options:
-n (number of individuals) 50
-L (number of loci) 400
-K (number of ancestral pops) 10
-x (genotype file) C:\Users\biocbuild\bbs-3.5-bioc\meat\LEA.Rcheck\examples_i386\genotypes.geno
-q (individual admixture) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K10/run10/genotypes_r10.10.Q
-g (ancestral frequencies) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/K10/run10/genotypes_r10.10.G
-i (with masked genotypes) C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/genotypes.snmf/masked/genotypes_I.geno
- diploid
Cross-Entropy (all data): 0.363902
Cross-Entropy (masked data): 0.752227
The project is saved into :
genotypes.snmfProject
To load the project, use:
project = load.snmfProject("genotypes.snmfProject")
To remove the project, use:
remove.snmfProject("genotypes.snmfProject")
>
> # plot cross-entropy criterion of all runs of the project
> plot(project, lwd = 5, col = "red", pch=1)
>
> # get the cross-entropy of each run for K = 4
> ce = cross.entropy(project, K = 4)
>
> # select the run with the lowest cross-entropy
> best = which.min(ce)
>
> # plot the best run for K = 4 (ancestry coefficients).
> barplot(t(Q(project, K = 4, run = best)))
>
> ###################
> # Post-treatments #
> ###################
>
> # show the project
> show(project)
snmf Project
snmfProject file: genotypes.snmfProject
project directory: C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/examples_i386/
snmf results directory: genotypes.snmf/
date of creation: 1502859126
input file: genotypes.geno
number of individuals: 50
number of loci: 400
number of ancestral populations: 1 2 3 4 5 6 7 8 9 10 1 2 3 4 5 6 7 8 9 10 1 2 3 4 5 6 7 8 9 10 1 2 3 4 5 6 7 8 9 10 1 2 3 4 5 6 7 8 9 10 1 2 3 4 5 6 7 8 9 10 1 2 3 4 5 6 7 8 9 10 1 2 3 4 5 6 7 8 9 10 1 2 3 4 5 6 7 8 9 10 1 2 3 4 5 6 7 8 9 10
***** run *****
snmf class
file directory: K1/run1/
Q output file: genotypes_r1.1.Q
G output file: genotypes_r1.1.G
snmfClass file: genotypes_r1.1.snmfClass
number of ancestral populations: 1
run number: 1
regularization parameter: 10
number of CPUs: 1
seed: 570175512
maximal number of iterations: 200
tolerance error: 1e-05
Q input file:
cross-Entropy: 0.5911252
***** run *****
snmf class
file directory: K2/run1/
Q output file: genotypes_r1.2.Q
G output file: genotypes_r1.2.G
snmfClass file: genotypes_r1.2.snmfClass
number of ancestral populations: 2
run number: 1
regularization parameter: 10
number of CPUs: 1
seed: 570175512
maximal number of iterations: 200
tolerance error: 1e-05
Q input file:
cross-Entropy: 0.5445603
***** run *****
snmf class
file directory: K3/run1/
Q output file: genotypes_r1.3.Q
G output file: genotypes_r1.3.G
snmfClass file: genotypes_r1.3.snmfClass
number of ancestral populations: 3
run number: 1
regularization parameter: 10
number of CPUs: 1
seed: 570175512
maximal number of iterations: 200
tolerance error: 1e-05
Q input file:
cross-Entropy: 0.503908
***** run *****
snmf class
file directory: K4/run1/
Q output file: genotypes_r1.4.Q
G output file: genotypes_r1.4.G
snmfClass file: genotypes_r1.4.snmfClass
number of ancestral populations: 4
run number: 1
regularization parameter: 10
number of CPUs: 1
seed: 570175512
maximal number of iterations: 200
tolerance error: 1e-05
Q input file:
cross-Entropy: 0.5067247
***** run *****
snmf class
file directory: K5/run1/
Q output file: genotypes_r1.5.Q
G output file: genotypes_r1.5.G
snmfClass file: genotypes_r1.5.snmfClass
number of ancestral populations: 5
run number: 1
regularization parameter: 10
number of CPUs: 1
seed: 570175512
maximal number of iterations: 200
tolerance error: 1e-05
Q input file:
cross-Entropy: 0.5274375
***** run *****
snmf class
file directory: K6/run1/
Q output file: genotypes_r1.6.Q
G output file: genotypes_r1.6.G
snmfClass file: genotypes_r1.6.snmfClass
number of ancestral populations: 6
run number: 1
regularization parameter: 10
number of CPUs: 1
seed: 570175512
maximal number of iterations: 200
tolerance error: 1e-05
Q input file:
cross-Entropy: 0.5861055
***** run *****
snmf class
file directory: K7/run1/
Q output file: genotypes_r1.7.Q
G output file: genotypes_r1.7.G
snmfClass file: genotypes_r1.7.snmfClass
number of ancestral populations: 7
run number: 1
regularization parameter: 10
number of CPUs: 1
seed: 570175512
maximal number of iterations: 200
tolerance error: 1e-05
Q input file:
cross-Entropy: 0.5479763
***** run *****
snmf class
file directory: K8/run1/
Q output file: genotypes_r1.8.Q
G output file: genotypes_r1.8.G
snmfClass file: genotypes_r1.8.snmfClass
number of ancestral populations: 8
run number: 1
regularization parameter: 10
number of CPUs: 1
seed: 570175512
maximal number of iterations: 200
tolerance error: 1e-05
Q input file:
cross-Entropy: 0.6136637
***** run *****
snmf class
file directory: K9/run1/
Q output file: genotypes_r1.9.Q
G output file: genotypes_r1.9.G
snmfClass file: genotypes_r1.9.snmfClass
number of ancestral populations: 9
run number: 1
regularization parameter: 10
number of CPUs: 1
seed: 570175512
maximal number of iterations: 200
tolerance error: 1e-05
Q input file:
cross-Entropy: 0.6318402
***** run *****
snmf class
file directory: K10/run1/
Q output file: genotypes_r1.10.Q
G output file: genotypes_r1.10.G
snmfClass file: genotypes_r1.10.snmfClass
number of ancestral populations: 10
run number: 1
regularization parameter: 10
number of CPUs: 1
seed: 570175512
maximal number of iterations: 200
tolerance error: 1e-05
Q input file:
cross-Entropy: 0.6241594
***** run *****
snmf class
file directory: K1/run2/
Q output file: genotypes_r2.1.Q
G output file: genotypes_r2.1.G
snmfClass file: genotypes_r2.1.snmfClass
number of ancestral populations: 1
run number: 2
regularization parameter: 10
number of CPUs: 1
seed: 1239947635
maximal number of iterations: 200
tolerance error: 1e-05
Q input file:
cross-Entropy: 0.6653946
***** run *****
snmf class
file directory: K2/run2/
Q output file: genotypes_r2.2.Q
G output file: genotypes_r2.2.G
snmfClass file: genotypes_r2.2.snmfClass
number of ancestral populations: 2
run number: 2
regularization parameter: 10
number of CPUs: 1
seed: 1239947635
maximal number of iterations: 200
tolerance error: 1e-05
Q input file:
cross-Entropy: 0.6458583
***** run *****
snmf class
file directory: K3/run2/
Q output file: genotypes_r2.3.Q
G output file: genotypes_r2.3.G
snmfClass file: genotypes_r2.3.snmfClass
number of ancestral populations: 3
run number: 2
regularization parameter: 10
number of CPUs: 1
seed: 1239947635
maximal number of iterations: 200
tolerance error: 1e-05
Q input file:
cross-Entropy: 0.6134063
***** run *****
snmf class
file directory: K4/run2/
Q output file: genotypes_r2.4.Q
G output file: genotypes_r2.4.G
snmfClass file: genotypes_r2.4.snmfClass
number of ancestral populations: 4
run number: 2
regularization parameter: 10
number of CPUs: 1
seed: 1239947635
maximal number of iterations: 200
tolerance error: 1e-05
Q input file:
cross-Entropy: 0.5972979
***** run *****
snmf class
file directory: K5/run2/
Q output file: genotypes_r2.5.Q
G output file: genotypes_r2.5.G
snmfClass file: genotypes_r2.5.snmfClass
number of ancestral populations: 5
run number: 2
regularization parameter: 10
number of CPUs: 1
seed: 1239947635
maximal number of iterations: 200
tolerance error: 1e-05
Q input file:
cross-Entropy: 0.6191697
***** run *****
snmf class
file directory: K6/run2/
Q output file: genotypes_r2.6.Q
G output file: genotypes_r2.6.G
snmfClass file: genotypes_r2.6.snmfClass
number of ancestral populations: 6
run number: 2
regularization parameter: 10
number of CPUs: 1
seed: 1239947635
maximal number of iterations: 200
tolerance error: 1e-05
Q input file:
cross-Entropy: 0.6458837
***** run *****
snmf class
file directory: K7/run2/
Q output file: genotypes_r2.7.Q
G output file: genotypes_r2.7.G
snmfClass file: genotypes_r2.7.snmfClass
number of ancestral populations: 7
run number: 2
regularization parameter: 10
number of CPUs: 1
seed: 1239947635
maximal number of iterations: 200
tolerance error: 1e-05
Q input file:
cross-Entropy: 0.6300213
***** run *****
snmf class
file directory: K8/run2/
Q output file: genotypes_r2.8.Q
G output file: genotypes_r2.8.G
snmfClass file: genotypes_r2.8.snmfClass
number of ancestral populations: 8
run number: 2
regularization parameter: 10
number of CPUs: 1
seed: 1239947635
maximal number of iterations: 200
tolerance error: 1e-05
Q input file:
cross-Entropy: 0.6569436
***** run *****
snmf class
file directory: K9/run2/
Q output file: genotypes_r2.9.Q
G output file: genotypes_r2.9.G
snmfClass file: genotypes_r2.9.snmfClass
number of ancestral populations: 9
run number: 2
regularization parameter: 10
number of CPUs: 1
seed: 1239947635
maximal number of iterations: 200
tolerance error: 1e-05
Q input file:
cross-Entropy: 0.6865689
***** run *****
snmf class
file directory: K10/run2/
Q output file: genotypes_r2.10.Q
G output file: genotypes_r2.10.G
snmfClass file: genotypes_r2.10.snmfClass
number of ancestral populations: 10
run number: 2
regularization parameter: 10
number of CPUs: 1
seed: 1239947635
maximal number of iterations: 200
tolerance error: 1e-05
Q input file:
cross-Entropy: 0.6687256
***** run *****
snmf class
file directory: K1/run3/
Q output file: genotypes_r3.1.Q
G output file: genotypes_r3.1.G
snmfClass file: genotypes_r3.1.snmfClass
number of ancestral populations: 1
run number: 3
regularization parameter: 10
number of CPUs: 1
seed: 1663831666
maximal number of iterations: 200
tolerance error: 1e-05
Q input file:
cross-Entropy: 0.5983274
***** run *****
snmf class
file directory: K2/run3/
Q output file: genotypes_r3.2.Q
G output file: genotypes_r3.2.G
snmfClass file: genotypes_r3.2.snmfClass
number of ancestral populations: 2
run number: 3
regularization parameter: 10
number of CPUs: 1
seed: 1663831666
maximal number of iterations: 200
tolerance error: 1e-05
Q input file:
cross-Entropy: 0.5714681
***** run *****
snmf class
file directory: K3/run3/
Q output file: genotypes_r3.3.Q
G output file: genotypes_r3.3.G
snmfClass file: genotypes_r3.3.snmfClass
number of ancestral populations: 3
run number: 3
regularization parameter: 10
number of CPUs: 1
seed: 1663831666
maximal number of iterations: 200
tolerance error: 1e-05
Q input file:
cross-Entropy: 0.5649433
***** run *****
snmf class
file directory: K4/run3/
Q output file: genotypes_r3.4.Q
G output file: genotypes_r3.4.G
snmfClass file: genotypes_r3.4.snmfClass
number of ancestral populations: 4
run number: 3
regularization parameter: 10
number of CPUs: 1
seed: 1663831666
maximal number of iterations: 200
tolerance error: 1e-05
Q input file:
cross-Entropy: 0.5708171
***** run *****
snmf class
file directory: K5/run3/
Q output file: genotypes_r3.5.Q
G output file: genotypes_r3.5.G
snmfClass file: genotypes_r3.5.snmfClass
number of ancestral populations: 5
run number: 3
regularization parameter: 10
number of CPUs: 1
seed: 1663831666
maximal number of iterations: 200
tolerance error: 1e-05
Q input file:
cross-Entropy: 0.6029688
***** run *****
snmf class
file directory: K6/run3/
Q output file: genotypes_r3.6.Q
G output file: genotypes_r3.6.G
snmfClass file: genotypes_r3.6.snmfClass
number of ancestral populations: 6
run number: 3
regularization parameter: 10
number of CPUs: 1
seed: 1663831666
maximal number of iterations: 200
tolerance error: 1e-05
Q input file:
cross-Entropy: 0.6005934
***** run *****
snmf class
file directory: K7/run3/
Q output file: genotypes_r3.7.Q
G output file: genotypes_r3.7.G
snmfClass file: genotypes_r3.7.snmfClass
number of ancestral populations: 7
run number: 3
regularization parameter: 10
number of CPUs: 1
seed: 1663831666
maximal number of iterations: 200
tolerance error: 1e-05
Q input file:
cross-Entropy: 0.6459744
***** run *****
snmf class
file directory: K8/run3/
Q output file: genotypes_r3.8.Q
G output file: genotypes_r3.8.G
snmfClass file: genotypes_r3.8.snmfClass
number of ancestral populations: 8
run number: 3
regularization parameter: 10
number of CPUs: 1
seed: 1663831666
maximal number of iterations: 200
tolerance error: 1e-05
Q input file:
cross-Entropy: 0.6614498
***** run *****
snmf class
file directory: K9/run3/
Q output file: genotypes_r3.9.Q
G output file: genotypes_r3.9.G
snmfClass file: genotypes_r3.9.snmfClass
number of ancestral populations: 9
run number: 3
regularization parameter: 10
number of CPUs: 1
seed: 1663831666
maximal number of iterations: 200
tolerance error: 1e-05
Q input file:
cross-Entropy: 0.6582306
***** run *****
snmf class
file directory: K10/run3/
Q output file: genotypes_r3.10.Q
G output file: genotypes_r3.10.G
snmfClass file: genotypes_r3.10.snmfClass
number of ancestral populations: 10
run number: 3
regularization parameter: 10
number of CPUs: 1
seed: 1663831666
maximal number of iterations: 200
tolerance error: 1e-05
Q input file:
cross-Entropy: 0.6809379
***** run *****
snmf class
file directory: K1/run4/
Q output file: genotypes_r4.1.Q
G output file: genotypes_r4.1.G
snmfClass file: genotypes_r4.1.snmfClass
number of ancestral populations: 1
run number: 4
regularization parameter: 10
number of CPUs: 1
seed: 978228245
maximal number of iterations: 200
tolerance error: 1e-05
Q input file:
cross-Entropy: 0.6533893
***** run *****
snmf class
file directory: K2/run4/
Q output file: genotypes_r4.2.Q
G output file: genotypes_r4.2.G
snmfClass file: genotypes_r4.2.snmfClass
number of ancestral populations: 2
run number: 4
regularization parameter: 10
number of CPUs: 1
seed: 978228245
maximal number of iterations: 200
tolerance error: 1e-05
Q input file:
cross-Entropy: 0.6226345
***** run *****
snmf class
file directory: K3/run4/
Q output file: genotypes_r4.3.Q
G output file: genotypes_r4.3.G
snmfClass file: genotypes_r4.3.snmfClass
number of ancestral populations: 3
run number: 4
regularization parameter: 10
number of CPUs: 1
seed: 978228245
maximal number of iterations: 200
tolerance error: 1e-05
Q input file:
cross-Entropy: 0.6278079
***** run *****
snmf class
file directory: K4/run4/
Q output file: genotypes_r4.4.Q
G output file: genotypes_r4.4.G
snmfClass file: genotypes_r4.4.snmfClass
number of ancestral populations: 4
run number: 4
regularization parameter: 10
number of CPUs: 1
seed: 978228245
maximal number of iterations: 200
tolerance error: 1e-05
Q input file:
cross-Entropy: 0.6278097
***** run *****
snmf class
file directory: K5/run4/
Q output file: genotypes_r4.5.Q
G output file: genotypes_r4.5.G
snmfClass file: genotypes_r4.5.snmfClass
number of ancestral populations: 5
run number: 4
regularization parameter: 10
number of CPUs: 1
seed: 978228245
maximal number of iterations: 200
tolerance error: 1e-05
Q input file:
cross-Entropy: 0.6561205
***** run *****
snmf class
file directory: K6/run4/
Q output file: genotypes_r4.6.Q
G output file: genotypes_r4.6.G
snmfClass file: genotypes_r4.6.snmfClass
number of ancestral populations: 6
run number: 4
regularization parameter: 10
number of CPUs: 1
seed: 978228245
maximal number of iterations: 200
tolerance error: 1e-05
Q input file:
cross-Entropy: 0.6480318
***** run *****
snmf class
file directory: K7/run4/
Q output file: genotypes_r4.7.Q
G output file: genotypes_r4.7.G
snmfClass file: genotypes_r4.7.snmfClass
number of ancestral populations: 7
run number: 4
regularization parameter: 10
number of CPUs: 1
seed: 978228245
maximal number of iterations: 200
tolerance error: 1e-05
Q input file:
cross-Entropy: 0.6709793
***** run *****
snmf class
file directory: K8/run4/
Q output file: genotypes_r4.8.Q
G output file: genotypes_r4.8.G
snmfClass file: genotypes_r4.8.snmfClass
number of ancestral populations: 8
run number: 4
regularization parameter: 10
number of CPUs: 1
seed: 978228245
maximal number of iterations: 200
tolerance error: 1e-05
Q input file:
cross-Entropy: 0.7041047
***** run *****
snmf class
file directory: K9/run4/
Q output file: genotypes_r4.9.Q
G output file: genotypes_r4.9.G
snmfClass file: genotypes_r4.9.snmfClass
number of ancestral populations: 9
run number: 4
regularization parameter: 10
number of CPUs: 1
seed: 978228245
maximal number of iterations: 200
tolerance error: 1e-05
Q input file:
cross-Entropy: 0.7416668
***** run *****
snmf class
file directory: K10/run4/
Q output file: genotypes_r4.10.Q
G output file: genotypes_r4.10.G
snmfClass file: genotypes_r4.10.snmfClass
number of ancestral populations: 10
run number: 4
regularization parameter: 10
number of CPUs: 1
seed: 978228245
maximal number of iterations: 200
tolerance error: 1e-05
Q input file:
cross-Entropy: 0.7708492
***** run *****
snmf class
file directory: K1/run5/
Q output file: genotypes_r5.1.Q
G output file: genotypes_r5.1.G
snmfClass file: genotypes_r5.1.snmfClass
number of ancestral populations: 1
run number: 5
regularization parameter: 10
number of CPUs: 1
seed: 1112635313
maximal number of iterations: 200
tolerance error: 1e-05
Q input file:
cross-Entropy: 0.6289054
***** run *****
snmf class
file directory: K2/run5/
Q output file: genotypes_r5.2.Q
G output file: genotypes_r5.2.G
snmfClass file: genotypes_r5.2.snmfClass
number of ancestral populations: 2
run number: 5
regularization parameter: 10
number of CPUs: 1
seed: 1112635313
maximal number of iterations: 200
tolerance error: 1e-05
Q input file:
cross-Entropy: 0.6151495
***** run *****
snmf class
file directory: K3/run5/
Q output file: genotypes_r5.3.Q
G output file: genotypes_r5.3.G
snmfClass file: genotypes_r5.3.snmfClass
number of ancestral populations: 3
run number: 5
regularization parameter: 10
number of CPUs: 1
seed: 1112635313
maximal number of iterations: 200
tolerance error: 1e-05
Q input file:
cross-Entropy: 0.5795091
***** run *****
snmf class
file directory: K4/run5/
Q output file: genotypes_r5.4.Q
G output file: genotypes_r5.4.G
snmfClass file: genotypes_r5.4.snmfClass
number of ancestral populations: 4
run number: 5
regularization parameter: 10
number of CPUs: 1
seed: 1112635313
maximal number of iterations: 200
tolerance error: 1e-05
Q input file:
cross-Entropy: 0.5927711
***** run *****
snmf class
file directory: K5/run5/
Q output file: genotypes_r5.5.Q
G output file: genotypes_r5.5.G
snmfClass file: genotypes_r5.5.snmfClass
number of ancestral populations: 5
run number: 5
regularization parameter: 10
number of CPUs: 1
seed: 1112635313
maximal number of iterations: 200
tolerance error: 1e-05
Q input file:
cross-Entropy: 0.5930789
***** run *****
snmf class
file directory: K6/run5/
Q output file: genotypes_r5.6.Q
G output file: genotypes_r5.6.G
snmfClass file: genotypes_r5.6.snmfClass
number of ancestral populations: 6
run number: 5
regularization parameter: 10
number of CPUs: 1
seed: 1112635313
maximal number of iterations: 200
tolerance error: 1e-05
Q input file:
cross-Entropy: 0.6265456
***** run *****
snmf class
file directory: K7/run5/
Q output file: genotypes_r5.7.Q
G output file: genotypes_r5.7.G
snmfClass file: genotypes_r5.7.snmfClass
number of ancestral populations: 7
run number: 5
regularization parameter: 10
number of CPUs: 1
seed: 1112635313
maximal number of iterations: 200
tolerance error: 1e-05
Q input file:
cross-Entropy: 0.6069716
***** run *****
snmf class
file directory: K8/run5/
Q output file: genotypes_r5.8.Q
G output file: genotypes_r5.8.G
snmfClass file: genotypes_r5.8.snmfClass
number of ancestral populations: 8
run number: 5
regularization parameter: 10
number of CPUs: 1
seed: 1112635313
maximal number of iterations: 200
tolerance error: 1e-05
Q input file:
cross-Entropy: 0.6495027
***** run *****
snmf class
file directory: K9/run5/
Q output file: genotypes_r5.9.Q
G output file: genotypes_r5.9.G
snmfClass file: genotypes_r5.9.snmfClass
number of ancestral populations: 9
run number: 5
regularization parameter: 10
number of CPUs: 1
seed: 1112635313
maximal number of iterations: 200
tolerance error: 1e-05
Q input file:
cross-Entropy: 0.7079227
***** run *****
snmf class
file directory: K10/run5/
Q output file: genotypes_r5.10.Q
G output file: genotypes_r5.10.G
snmfClass file: genotypes_r5.10.snmfClass
number of ancestral populations: 10
run number: 5
regularization parameter: 10
number of CPUs: 1
seed: 1112635313
maximal number of iterations: 200
tolerance error: 1e-05
Q input file:
cross-Entropy: 0.7542203
***** run *****
snmf class
file directory: K1/run6/
Q output file: genotypes_r6.1.Q
G output file: genotypes_r6.1.G
snmfClass file: genotypes_r6.1.snmfClass
number of ancestral populations: 1
run number: 6
regularization parameter: 10
number of CPUs: 1
seed: 2118848436
maximal number of iterations: 200
tolerance error: 1e-05
Q input file:
cross-Entropy: 0.632533
***** run *****
snmf class
file directory: K2/run6/
Q output file: genotypes_r6.2.Q
G output file: genotypes_r6.2.G
snmfClass file: genotypes_r6.2.snmfClass
number of ancestral populations: 2
run number: 6
regularization parameter: 10
number of CPUs: 1
seed: 2118848436
maximal number of iterations: 200
tolerance error: 1e-05
Q input file:
cross-Entropy: 0.5887809
***** run *****
snmf class
file directory: K3/run6/
Q output file: genotypes_r6.3.Q
G output file: genotypes_r6.3.G
snmfClass file: genotypes_r6.3.snmfClass
number of ancestral populations: 3
run number: 6
regularization parameter: 10
number of CPUs: 1
seed: 2118848436
maximal number of iterations: 200
tolerance error: 1e-05
Q input file:
cross-Entropy: 0.5624828
***** run *****
snmf class
file directory: K4/run6/
Q output file: genotypes_r6.4.Q
G output file: genotypes_r6.4.G
snmfClass file: genotypes_r6.4.snmfClass
number of ancestral populations: 4
run number: 6
regularization parameter: 10
number of CPUs: 1
seed: 2118848436
maximal number of iterations: 200
tolerance error: 1e-05
Q input file:
cross-Entropy: 0.5542967
***** run *****
snmf class
file directory: K5/run6/
Q output file: genotypes_r6.5.Q
G output file: genotypes_r6.5.G
snmfClass file: genotypes_r6.5.snmfClass
number of ancestral populations: 5
run number: 6
regularization parameter: 10
number of CPUs: 1
seed: 2118848436
maximal number of iterations: 200
tolerance error: 1e-05
Q input file:
cross-Entropy: 0.5513784
***** run *****
snmf class
file directory: K6/run6/
Q output file: genotypes_r6.6.Q
G output file: genotypes_r6.6.G
snmfClass file: genotypes_r6.6.snmfClass
number of ancestral populations: 6
run number: 6
regularization parameter: 10
number of CPUs: 1
seed: 2118848436
maximal number of iterations: 200
tolerance error: 1e-05
Q input file:
cross-Entropy: 0.5700338
***** run *****
snmf class
file directory: K7/run6/
Q output file: genotypes_r6.7.Q
G output file: genotypes_r6.7.G
snmfClass file: genotypes_r6.7.snmfClass
number of ancestral populations: 7
run number: 6
regularization parameter: 10
number of CPUs: 1
seed: 2118848436
maximal number of iterations: 200
tolerance error: 1e-05
Q input file:
cross-Entropy: 0.6103685
***** run *****
snmf class
file directory: K8/run6/
Q output file: genotypes_r6.8.Q
G output file: genotypes_r6.8.G
snmfClass file: genotypes_r6.8.snmfClass
number of ancestral populations: 8
run number: 6
regularization parameter: 10
number of CPUs: 1
seed: 2118848436
maximal number of iterations: 200
tolerance error: 1e-05
Q input file:
cross-Entropy: 0.6084052
***** run *****
snmf class
file directory: K9/run6/
Q output file: genotypes_r6.9.Q
G output file: genotypes_r6.9.G
snmfClass file: genotypes_r6.9.snmfClass
number of ancestral populations: 9
run number: 6
regularization parameter: 10
number of CPUs: 1
seed: 2118848436
maximal number of iterations: 200
tolerance error: 1e-05
Q input file:
cross-Entropy: 0.6594202
***** run *****
snmf class
file directory: K10/run6/
Q output file: genotypes_r6.10.Q
G output file: genotypes_r6.10.G
snmfClass file: genotypes_r6.10.snmfClass
number of ancestral populations: 10
run number: 6
regularization parameter: 10
number of CPUs: 1
seed: 2118848436
maximal number of iterations: 200
tolerance error: 1e-05
Q input file:
cross-Entropy: 0.6708666
***** run *****
snmf class
file directory: K1/run7/
Q output file: genotypes_r7.1.Q
G output file: genotypes_r7.1.G
snmfClass file: genotypes_r7.1.snmfClass
number of ancestral populations: 1
run number: 7
regularization parameter: 10
number of CPUs: 1
seed: 1105185580
maximal number of iterations: 200
tolerance error: 1e-05
Q input file:
cross-Entropy: 0.6219842
***** run *****
snmf class
file directory: K2/run7/
Q output file: genotypes_r7.2.Q
G output file: genotypes_r7.2.G
snmfClass file: genotypes_r7.2.snmfClass
number of ancestral populations: 2
run number: 7
regularization parameter: 10
number of CPUs: 1
seed: 1105185580
maximal number of iterations: 200
tolerance error: 1e-05
Q input file:
cross-Entropy: 0.5784268
***** run *****
snmf class
file directory: K3/run7/
Q output file: genotypes_r7.3.Q
G output file: genotypes_r7.3.G
snmfClass file: genotypes_r7.3.snmfClass
number of ancestral populations: 3
run number: 7
regularization parameter: 10
number of CPUs: 1
seed: 1105185580
maximal number of iterations: 200
tolerance error: 1e-05
Q input file:
cross-Entropy: 0.5692388
***** run *****
snmf class
file directory: K4/run7/
Q output file: genotypes_r7.4.Q
G output file: genotypes_r7.4.G
snmfClass file: genotypes_r7.4.snmfClass
number of ancestral populations: 4
run number: 7
regularization parameter: 10
number of CPUs: 1
seed: 1105185580
maximal number of iterations: 200
tolerance error: 1e-05
Q input file:
cross-Entropy: 0.5663857
***** run *****
snmf class
file directory: K5/run7/
Q output file: genotypes_r7.5.Q
G output file: genotypes_r7.5.G
snmfClass file: genotypes_r7.5.snmfClass
number of ancestral populations: 5
run number: 7
regularization parameter: 10
number of CPUs: 1
seed: 1105185580
maximal number of iterations: 200
tolerance error: 1e-05
Q input file:
cross-Entropy: 0.6060159
***** run *****
snmf class
file directory: K6/run7/
Q output file: genotypes_r7.6.Q
G output file: genotypes_r7.6.G
snmfClass file: genotypes_r7.6.snmfClass
number of ancestral populations: 6
run number: 7
regularization parameter: 10
number of CPUs: 1
seed: 1105185580
maximal number of iterations: 200
tolerance error: 1e-05
Q input file:
cross-Entropy: 0.610178
***** run *****
snmf class
file directory: K7/run7/
Q output file: genotypes_r7.7.Q
G output file: genotypes_r7.7.G
snmfClass file: genotypes_r7.7.snmfClass
number of ancestral populations: 7
run number: 7
regularization parameter: 10
number of CPUs: 1
seed: 1105185580
maximal number of iterations: 200
tolerance error: 1e-05
Q input file:
cross-Entropy: 0.6777445
***** run *****
snmf class
file directory: K8/run7/
Q output file: genotypes_r7.8.Q
G output file: genotypes_r7.8.G
snmfClass file: genotypes_r7.8.snmfClass
number of ancestral populations: 8
run number: 7
regularization parameter: 10
number of CPUs: 1
seed: 1105185580
maximal number of iterations: 200
tolerance error: 1e-05
Q input file:
cross-Entropy: 0.6806522
***** run *****
snmf class
file directory: K9/run7/
Q output file: genotypes_r7.9.Q
G output file: genotypes_r7.9.G
snmfClass file: genotypes_r7.9.snmfClass
number of ancestral populations: 9
run number: 7
regularization parameter: 10
number of CPUs: 1
seed: 1105185580
maximal number of iterations: 200
tolerance error: 1e-05
Q input file:
cross-Entropy: 0.7088885
***** run *****
snmf class
file directory: K10/run7/
Q output file: genotypes_r7.10.Q
G output file: genotypes_r7.10.G
snmfClass file: genotypes_r7.10.snmfClass
number of ancestral populations: 10
run number: 7
regularization parameter: 10
number of CPUs: 1
seed: 1105185580
maximal number of iterations: 200
tolerance error: 1e-05
Q input file:
cross-Entropy: 0.7387753
***** run *****
snmf class
file directory: K1/run8/
Q output file: genotypes_r8.1.Q
G output file: genotypes_r8.1.G
snmfClass file: genotypes_r8.1.snmfClass
number of ancestral populations: 1
run number: 8
regularization parameter: 10
number of CPUs: 1
seed: 1947026275
maximal number of iterations: 200
tolerance error: 1e-05
Q input file:
cross-Entropy: 0.6649313
***** run *****
snmf class
file directory: K2/run8/
Q output file: genotypes_r8.2.Q
G output file: genotypes_r8.2.G
snmfClass file: genotypes_r8.2.snmfClass
number of ancestral populations: 2
run number: 8
regularization parameter: 10
number of CPUs: 1
seed: 1947026275
maximal number of iterations: 200
tolerance error: 1e-05
Q input file:
cross-Entropy: 0.6383261
***** run *****
snmf class
file directory: K3/run8/
Q output file: genotypes_r8.3.Q
G output file: genotypes_r8.3.G
snmfClass file: genotypes_r8.3.snmfClass
number of ancestral populations: 3
run number: 8
regularization parameter: 10
number of CPUs: 1
seed: 1947026275
maximal number of iterations: 200
tolerance error: 1e-05
Q input file:
cross-Entropy: 0.607649
***** run *****
snmf class
file directory: K4/run8/
Q output file: genotypes_r8.4.Q
G output file: genotypes_r8.4.G
snmfClass file: genotypes_r8.4.snmfClass
number of ancestral populations: 4
run number: 8
regularization parameter: 10
number of CPUs: 1
seed: 1947026275
maximal number of iterations: 200
tolerance error: 1e-05
Q input file:
cross-Entropy: 0.6193417
***** run *****
snmf class
file directory: K5/run8/
Q output file: genotypes_r8.5.Q
G output file: genotypes_r8.5.G
snmfClass file: genotypes_r8.5.snmfClass
number of ancestral populations: 5
run number: 8
regularization parameter: 10
number of CPUs: 1
seed: 1947026275
maximal number of iterations: 200
tolerance error: 1e-05
Q input file:
cross-Entropy: 0.6024201
***** run *****
snmf class
file directory: K6/run8/
Q output file: genotypes_r8.6.Q
G output file: genotypes_r8.6.G
snmfClass file: genotypes_r8.6.snmfClass
number of ancestral populations: 6
run number: 8
regularization parameter: 10
number of CPUs: 1
seed: 1947026275
maximal number of iterations: 200
tolerance error: 1e-05
Q input file:
cross-Entropy: 0.6290001
***** run *****
snmf class
file directory: K7/run8/
Q output file: genotypes_r8.7.Q
G output file: genotypes_r8.7.G
snmfClass file: genotypes_r8.7.snmfClass
number of ancestral populations: 7
run number: 8
regularization parameter: 10
number of CPUs: 1
seed: 1947026275
maximal number of iterations: 200
tolerance error: 1e-05
Q input file:
cross-Entropy: 0.6583155
***** run *****
snmf class
file directory: K8/run8/
Q output file: genotypes_r8.8.Q
G output file: genotypes_r8.8.G
snmfClass file: genotypes_r8.8.snmfClass
number of ancestral populations: 8
run number: 8
regularization parameter: 10
number of CPUs: 1
seed: 1947026275
maximal number of iterations: 200
tolerance error: 1e-05
Q input file:
cross-Entropy: 0.6889163
***** run *****
snmf class
file directory: K9/run8/
Q output file: genotypes_r8.9.Q
G output file: genotypes_r8.9.G
snmfClass file: genotypes_r8.9.snmfClass
number of ancestral populations: 9
run number: 8
regularization parameter: 10
number of CPUs: 1
seed: 1947026275
maximal number of iterations: 200
tolerance error: 1e-05
Q input file:
cross-Entropy: 0.7484452
***** run *****
snmf class
file directory: K10/run8/
Q output file: genotypes_r8.10.Q
G output file: genotypes_r8.10.G
snmfClass file: genotypes_r8.10.snmfClass
number of ancestral populations: 10
run number: 8
regularization parameter: 10
number of CPUs: 1
seed: 1947026275
maximal number of iterations: 200
tolerance error: 1e-05
Q input file:
cross-Entropy: 0.7491888
***** run *****
snmf class
file directory: K1/run9/
Q output file: genotypes_r9.1.Q
G output file: genotypes_r9.1.G
snmfClass file: genotypes_r9.1.snmfClass
number of ancestral populations: 1
run number: 9
regularization parameter: 10
number of CPUs: 1
seed: 942839743
maximal number of iterations: 200
tolerance error: 1e-05
Q input file:
cross-Entropy: 0.6926317
***** run *****
snmf class
file directory: K2/run9/
Q output file: genotypes_r9.2.Q
G output file: genotypes_r9.2.G
snmfClass file: genotypes_r9.2.snmfClass
number of ancestral populations: 2
run number: 9
regularization parameter: 10
number of CPUs: 1
seed: 942839743
maximal number of iterations: 200
tolerance error: 1e-05
Q input file:
cross-Entropy: 0.6565924
***** run *****
snmf class
file directory: K3/run9/
Q output file: genotypes_r9.3.Q
G output file: genotypes_r9.3.G
snmfClass file: genotypes_r9.3.snmfClass
number of ancestral populations: 3
run number: 9
regularization parameter: 10
number of CPUs: 1
seed: 942839743
maximal number of iterations: 200
tolerance error: 1e-05
Q input file:
cross-Entropy: 0.6497421
***** run *****
snmf class
file directory: K4/run9/
Q output file: genotypes_r9.4.Q
G output file: genotypes_r9.4.G
snmfClass file: genotypes_r9.4.snmfClass
number of ancestral populations: 4
run number: 9
regularization parameter: 10
number of CPUs: 1
seed: 942839743
maximal number of iterations: 200
tolerance error: 1e-05
Q input file:
cross-Entropy: 0.6249767
***** run *****
snmf class
file directory: K5/run9/
Q output file: genotypes_r9.5.Q
G output file: genotypes_r9.5.G
snmfClass file: genotypes_r9.5.snmfClass
number of ancestral populations: 5
run number: 9
regularization parameter: 10
number of CPUs: 1
seed: 942839743
maximal number of iterations: 200
tolerance error: 1e-05
Q input file:
cross-Entropy: 0.6293201
***** run *****
snmf class
file directory: K6/run9/
Q output file: genotypes_r9.6.Q
G output file: genotypes_r9.6.G
snmfClass file: genotypes_r9.6.snmfClass
number of ancestral populations: 6
run number: 9
regularization parameter: 10
number of CPUs: 1
seed: 942839743
maximal number of iterations: 200
tolerance error: 1e-05
Q input file:
cross-Entropy: 0.6898999
***** run *****
snmf class
file directory: K7/run9/
Q output file: genotypes_r9.7.Q
G output file: genotypes_r9.7.G
snmfClass file: genotypes_r9.7.snmfClass
number of ancestral populations: 7
run number: 9
regularization parameter: 10
number of CPUs: 1
seed: 942839743
maximal number of iterations: 200
tolerance error: 1e-05
Q input file:
cross-Entropy: 0.7043437
***** run *****
snmf class
file directory: K8/run9/
Q output file: genotypes_r9.8.Q
G output file: genotypes_r9.8.G
snmfClass file: genotypes_r9.8.snmfClass
number of ancestral populations: 8
run number: 9
regularization parameter: 10
number of CPUs: 1
seed: 942839743
maximal number of iterations: 200
tolerance error: 1e-05
Q input file:
cross-Entropy: 0.706284
***** run *****
snmf class
file directory: K9/run9/
Q output file: genotypes_r9.9.Q
G output file: genotypes_r9.9.G
snmfClass file: genotypes_r9.9.snmfClass
number of ancestral populations: 9
run number: 9
regularization parameter: 10
number of CPUs: 1
seed: 942839743
maximal number of iterations: 200
tolerance error: 1e-05
Q input file:
cross-Entropy: 0.8048607
***** run *****
snmf class
file directory: K10/run9/
Q output file: genotypes_r9.10.Q
G output file: genotypes_r9.10.G
snmfClass file: genotypes_r9.10.snmfClass
number of ancestral populations: 10
run number: 9
regularization parameter: 10
number of CPUs: 1
seed: 942839743
maximal number of iterations: 200
tolerance error: 1e-05
Q input file:
cross-Entropy: 0.7771786
***** run *****
snmf class
file directory: K1/run10/
Q output file: genotypes_r10.1.Q
G output file: genotypes_r10.1.G
snmfClass file: genotypes_r10.1.snmfClass
number of ancestral populations: 1
run number: 10
regularization parameter: 10
number of CPUs: 1
seed: 1191190572
maximal number of iterations: 200
tolerance error: 1e-05
Q input file:
cross-Entropy: 0.6514754
***** run *****
snmf class
file directory: K2/run10/
Q output file: genotypes_r10.2.Q
G output file: genotypes_r10.2.G
snmfClass file: genotypes_r10.2.snmfClass
number of ancestral populations: 2
run number: 10
regularization parameter: 10
number of CPUs: 1
seed: 1191190572
maximal number of iterations: 200
tolerance error: 1e-05
Q input file:
cross-Entropy: 0.6398512
***** run *****
snmf class
file directory: K3/run10/
Q output file: genotypes_r10.3.Q
G output file: genotypes_r10.3.G
snmfClass file: genotypes_r10.3.snmfClass
number of ancestral populations: 3
run number: 10
regularization parameter: 10
number of CPUs: 1
seed: 1191190572
maximal number of iterations: 200
tolerance error: 1e-05
Q input file:
cross-Entropy: 0.5850677
***** run *****
snmf class
file directory: K4/run10/
Q output file: genotypes_r10.4.Q
G output file: genotypes_r10.4.G
snmfClass file: genotypes_r10.4.snmfClass
number of ancestral populations: 4
run number: 10
regularization parameter: 10
number of CPUs: 1
seed: 1191190572
maximal number of iterations: 200
tolerance error: 1e-05
Q input file:
cross-Entropy: 0.5976989
***** run *****
snmf class
file directory: K5/run10/
Q output file: genotypes_r10.5.Q
G output file: genotypes_r10.5.G
snmfClass file: genotypes_r10.5.snmfClass
number of ancestral populations: 5
run number: 10
regularization parameter: 10
number of CPUs: 1
seed: 1191190572
maximal number of iterations: 200
tolerance error: 1e-05
Q input file:
cross-Entropy: 0.6167047
***** run *****
snmf class
file directory: K6/run10/
Q output file: genotypes_r10.6.Q
G output file: genotypes_r10.6.G
snmfClass file: genotypes_r10.6.snmfClass
number of ancestral populations: 6
run number: 10
regularization parameter: 10
number of CPUs: 1
seed: 1191190572
maximal number of iterations: 200
tolerance error: 1e-05
Q input file:
cross-Entropy: 0.6379849
***** run *****
snmf class
file directory: K7/run10/
Q output file: genotypes_r10.7.Q
G output file: genotypes_r10.7.G
snmfClass file: genotypes_r10.7.snmfClass
number of ancestral populations: 7
run number: 10
regularization parameter: 10
number of CPUs: 1
seed: 1191190572
maximal number of iterations: 200
tolerance error: 1e-05
Q input file:
cross-Entropy: 0.6328526
***** run *****
snmf class
file directory: K8/run10/
Q output file: genotypes_r10.8.Q
G output file: genotypes_r10.8.G
snmfClass file: genotypes_r10.8.snmfClass
number of ancestral populations: 8
run number: 10
regularization parameter: 10
number of CPUs: 1
seed: 1191190572
maximal number of iterations: 200
tolerance error: 1e-05
Q input file:
cross-Entropy: 0.7100303
***** run *****
snmf class
file directory: K9/run10/
Q output file: genotypes_r10.9.Q
G output file: genotypes_r10.9.G
snmfClass file: genotypes_r10.9.snmfClass
number of ancestral populations: 9
run number: 10
regularization parameter: 10
number of CPUs: 1
seed: 1191190572
maximal number of iterations: 200
tolerance error: 1e-05
Q input file:
cross-Entropy: 0.7600355
***** run *****
snmf class
file directory: K10/run10/
Q output file: genotypes_r10.10.Q
G output file: genotypes_r10.10.G
snmfClass file: genotypes_r10.10.snmfClass
number of ancestral populations: 10
run number: 10
regularization parameter: 10
number of CPUs: 1
seed: 1191190572
maximal number of iterations: 200
tolerance error: 1e-05
Q input file:
cross-Entropy: 0.7522273
>
> # summary of the project
> summary(project)
$repetitions
K = 1 K = 2 K = 3 K = 4 K = 5 K = 6 K = 7 K = 8 K = 9
with cross-entropy 10 10 10 10 10 10 10 10 10
without cross-entropy 0 0 0 0 0 0 0 0 0
total 10 10 10 10 10 10 10 10 10
K = 10
with cross-entropy 10
without cross-entropy 0
total 10
$crossEntropy
K = 1 K = 2 K = 3 K = 4 K = 5 K = 6 K = 7
min 0.5911252 0.5445603 0.5039080 0.5067247 0.5274375 0.5700338 0.5479763
mean 0.6400697 0.6101648 0.5863755 0.5858120 0.6004615 0.6244257 0.6385548
max 0.6926317 0.6565924 0.6497421 0.6278097 0.6561205 0.6898999 0.7043437
K = 8 K = 9 K = 10
min 0.6084052 0.6318402 0.6241594
mean 0.6679952 0.7107879 0.7187129
max 0.7100303 0.8048607 0.7771786
>
> # get the cross-entropy for all runs for K = 4
> ce = cross.entropy(project, K = 4)
>
> # get the cross-entropy for the 2nd run for K = 4
> ce = cross.entropy(project, K = 4, run = 2)
>
> # get the ancestral genotype frequency matrix, G, for the 2nd run for K = 4.
> res = G(project, K = 4, run = 2)
>
> #############################
> # Advanced snmf run options #
> #############################
>
> # Q.input.file: init a run with a given ancestry coefficient matrix Q.
> # Here, it is initialized with the Q matrix from the first run with K=4
> project = snmf("genotypes.geno", K = 4,
+ Q.input.file = "./genotypes.snmf/K4/run1/genotypes_r1.4.Q")
Error in projectSnmfLoad(input.file, project) :
The input file has been modified since the creation of the project.
If the input file is different, the results concatenating all runs can be false.
To remove the current project and start a new one, add the option 'project = new'.
To continue with the same project, add the option 'project = force'.
Calls: snmf -> projectSnmfLoad
Execution halted
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
main_LFMM 85.59 0.07 88.72
main_sNMF 19.97 6.34 56.81
adjusted_pvalues 13.00 0.02 13.12
zscores 12.53 0.03 12.56
pvalues 11.64 0.01 11.66
mlog10pvalues 11.46 0.02 11.49
readZscore 5.92 0.02 5.94
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in 'inst/doc' ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: 1 ERROR, 1 NOTE
See
'C:/Users/biocbuild/bbs-3.5-bioc/meat/LEA.Rcheck/00check.log'
for details.
