lme.batch {GWAF}R Documentation

function to test genetic association for a continuous trait in families using Linear Mixed Effects model

Description

Fit linear mixed effect model to test association between a continuous phenotype and all SNPs in a genotype file with user specified genetic model. The SNP genotype is treated as fixed effects, and a random effect correlated according to degree of relatedness within a family is also fitted. In each trait-SNP assocaition test, the lmekin() function which is modified from the same named function in package kinship is used.

Usage

lme.batch(phenfile, genfile, pedfile, phen, kinmat, model = "a", 
covars = NULL, outfile)

Arguments

genfile a character string naming the genotype file for reading (see format requirement in details)
phenfile a character string naming the phenotype file for reading (see format requirement in details)
pedfile a character string naming the pedigree file for reading (see format requirement in details)
outfile a character string naming the result file for writing
phen a character string for a phenotype name in phenfile
covars a character vector for covariates in phenfile
model a single character of 'a','d','g', or 'r', with 'a'=additive, 'd'=dominant, 'g'=general and 'r'=recessive models
kinmat a character string naming the file where kinship coefficient matrix is kept

Details

The lme.batch function first reads in and merges comma-delimited phenotype-covariates, genotype and pedigree files, then tests the association of phen against all SNPs in genfile. genfile is a comma delimited file, with the column names being "id" and SNP names separated by comma. For each SNP, the genotype data should be coded as 0, 1, 2 indicating the numbers of less frequent alleles. The SNP name in genotype file should not have any dash, '-' and other special characters(dots and underscores are OK). phenfile is a comma delimited file, with the column names being "id" and phenotype and covaraite names separated by comma. pedfile is a comma delimited file, with the column names being "famid","id","fa","mo","sex". In all files, missing value should be an empty space. SNPs with low genotype counts (especially minor allele homozygote) may be omitted or analyzed with dominant model. The 'lme.batch' function fits linear mixed effects (LME) model using with 'lme.batch' function from GWAF package and a modified 'lmekin' function from kinship package.

Value

No value is returned. Instead, results are written to outfile. When the genetic model is 'a', 'd' or 'r', the result includes the following columns. When the genetic model is 'g', beta and se are replaced with beta10, beta20,beta21,se10,se20,se21 .

phen phenotype name
snp SNP name
n0 the number of individuals with 0 copy of minor alleles
n1 the number of individuals with 1 copy of minor alleles
n2 the number of individuals with 2 copies of minor alleles
h2q the portion of phenotypic variation explained by the SNP
beta regression coefficient of SNP covariate
se standard error of beta
chisq Chi-square statistic for testing beta not equal to zero
df degree of freedom of the Chi-square statistic
model model actually used in the analysis
pval p-value of the chi-square statistic
beta10 regression coefficient of genotype with 1 copy of minor allele vs. that with 0 copy
beta20 regression coefficient of genotype with 2 copy of minor allele vs. that with 0 copy
beta21 regression coefficient of genotype with 2 copy of minor allele vs. that with 1 copy
se10 standard error of beta10
se20 standard error of beta20
se21 standard error of beta21

Author(s)

Qiong Yang <qyang@bu.edu> and Ming-Huei Chen <mhchen@bu.edu>

References

kinship package: mixed-effects Cox models, sparse matrices, and modeling data from large pedigrees. Beth Atkinson (atkinson@mayo.edu) for pedigree functions.Terry Therneau (therneau@mayo.edu) for all other functions. 2007. Ref Type: Computer Program http://cran.r-project.org/.

Abecasis, G. R., Cardon, L. R., Cookson, W. O., Sham, P. C., & Cherny, S. S. Association analysis in a variance components framework. Genet Epidemiol, 21 Suppl 1, S341-S346 (2001).


[Package GWAF version 1.1 Index]