## ----style, eval=TRUE, echo=FALSE,results="asis"-------------------------
#library("BiocStyle")
BiocStyle::latex()


## ----setup, include=FALSE, cache=FALSE, echo=F---------------------------
library(knitr)
opts_chunk$set(fig.path='figure/minimal-', fig.align='center', fig.show='hold')
options(replace.assign=TRUE,width=90)


## ----citatation----------------------------------------------------------
citation(package='coMET')


## ----installPackages,eval=FALSE------------------------------------------
## source("http://bioconductor.org/biocLite.R")
## biocLite("coMET")


## ----dd,echo=FALSE,eval=FALSE--------------------------------------------
## require("hash")
## require("grid")
## require("grDevices")
## require("biomaRt")
## require("Gviz")
## require("ggbio")
## require("rtracklayer")
## require("GenomicRanges")
## require("colortools")
## require("gridExtra")
## require("ggplot2")
## require("trackViewer")
## require("psych")
## 
## rdir <- system.file("R", package="coMET",mustWork=TRUE)
## source(file.path(rdir, "AnalyseFile.R"))
## source(file.path(rdir, "BiofeatureGraphics.R"))
## source(file.path(rdir, "comet.R"))
## source(file.path(rdir, "cometWeb.R"))
## source(file.path(rdir, "DrawPlot.R"))
## source(file.path(rdir, "GeneralMethodComet.R"))


## ----loadPackages, eval=TRUE---------------------------------------------
library("coMET")


## ----findHel, eval=FALSE-------------------------------------------------
## ?comet
## ?comet.web
## ?comet.list


## ----installPackages_develbioc,eval=FALSE--------------------------------
## source("http://bioconductor.org/biocLite.R")
## biocLite("coMET")


## ----installPackages_develversion,eval=FALSE-----------------------------
## install.packages("YourPath/coMET_YourVersion.tar.gz",repos=NULL,type="source")
## ##This is an example
## install.packages("YourPath/coMET_0.99.9.tar.gz",repos=NULL,type="source")


## ----Filedata------------------------------------------------------------
extdata <- system.file("extdata", package="coMET",mustWork=TRUE)
infofile <- file.path(extdata, "cyp1b1_infofile.txt")

data_info <-read.csv(infofile, header = TRUE,
                     sep = "\t", quote = "")

head(data_info)


## ----expMatrix-----------------------------------------------------------
extdata <- system.file("extdata", package="coMET",mustWork=TRUE)
infoexp <- file.path(extdata, "cyp1b1_infofile_exprGene_region.txt")

data_infoexp <-read.csv(infoexp, header = TRUE,
                        sep = "\t", quote = "")

head(data_infoexp)


## ----corrMatrix----------------------------------------------------------
extdata <- system.file("extdata", package="coMET",mustWork=TRUE)
corfile <- file.path(extdata, "cyp1b1_res37_rawMatrix.txt")

data_cor <-read.csv(corfile, header = TRUE,
                    sep = "\t", quote = "")
data_cor[1:6,1:6]


## ----configMatrix--------------------------------------------------------
extdata <- system.file("extdata", package="coMET",mustWork=TRUE)
configfile <- file.path(extdata, "config_cyp1b1_zoom_4webserver.txt")

data_config <-read.csv(configfile, quote = "", sep="\t", header=FALSE)
data_config


## ----cometwebPlotText, eval=FALSE, fig.keep='last'-----------------------
## extdata <- system.file("extdata", package="coMET",mustWork=TRUE)
## myinfofile <- file.path(extdata, "cyp1b1_infofile.txt")
## myexpressfile <- file.path(extdata, "cyp1b1_infofile_exprGene_region.txt")
## mycorrelation <- file.path(extdata, "cyp1b1_res37_rawMatrix.txt")
## configfile <- file.path(extdata, "config_cyp1b1_zoom_4webserver.txt")
## comet.web(config.file=configfile, mydata.file=myinfofile,
##           cormatrix.file=mycorrelation ,mydata.large.file=myexpressfile,
##           print.image=FALSE,verbose=FALSE)


## ----cometwebPlot, echo=FALSE, fig.keep='last'---------------------------
extdata <- system.file("extdata", package="coMET",mustWork=TRUE)
myinfofile <- file.path(extdata, "cyp1b1_infofile.txt")
myexpressfile <- file.path(extdata, "cyp1b1_infofile_exprGene_region.txt")
mycorrelation <- file.path(extdata, "cyp1b1_res37_rawMatrix.txt") 
configfile <- file.path(extdata, "config_cyp1b1_zoom_4webserver.txt")
comet.web(config.file=configfile, mydata.file=myinfofile, cormatrix.file=mycorrelation,
          mydata.large.file=myexpressfile, print.image=FALSE,verbose=FALSE)


## ----cometPlotText, eval=FALSE, fig.keep='last'--------------------------
## extdata <- system.file("extdata", package="coMET",mustWork=TRUE)
## configfile <- file.path(extdata, "config_cyp1b1_zoom_4comet.txt")
## myinfofile <- file.path(extdata, "cyp1b1_infofile.txt")
## myexpressfile <- file.path(extdata, "cyp1b1_infofile_exprGene_region.txt")
## mycorrelation <- file.path(extdata, "cyp1b1_res37_rawMatrix.txt")
## 
## chrom <- "chr2"
## start <- 38290160
## end <- 38303219
## gen <- "hg19"
## strand <- "*"
## 
## BROWSER.SESSION="UCSC"
## mySession <- browserSession(BROWSER.SESSION)
## genome(mySession) <- gen
## 
## genetrack <-genesENSEMBL(gen,chrom,start,end,showId=TRUE)
## snptrack <- snpBiomart(chrom, start, end, dataset="hsapiens_snp_som",showId=FALSE)
## iscatrack <-ISCATrack(gen,chrom,start,end,mySession, table="iscaPathogenic")
## 
## listgviz <- list(genetrack,snptrack,iscatrack)
## 
## comet(config.file=configfile, mydata.file=myinfofile, mydata.type="file",
##       cormatrix.file=mycorrelation,  cormatrix.type="listfile",
##       mydata.large.file=myexpressfile, mydata.large.type="listfile",
##       tracks.gviz=listgviz, verbose=FALSE, print.image=FALSE)


## ----cometPlotfile, echo=FALSE, fig.keep='last'--------------------------
extdata <- system.file("extdata", package="coMET",mustWork=TRUE)
configfile <- file.path(extdata, "config_cyp1b1_zoom_4comet.txt")
myinfofile <- file.path(extdata, "cyp1b1_infofile.txt")
myexpressfile <- file.path(extdata, "cyp1b1_infofile_exprGene_region.txt")
mycorrelation <- file.path(extdata, "cyp1b1_res37_rawMatrix.txt")

#configfile <- "../inst/extdata/config_cyp1b1_zoom_4comet.txt" 
chrom <- "chr2"
start <- 38290160
end <- 38303219
gen <- "hg19"
strand <- "*"

data(geneENSEMBLtrack)
data(snpBiomarttrack)
data(ISCAtrack)

listgviz <- list(genetrack,snptrack,iscatrack)

comet(config.file=configfile, mydata.file=myinfofile, mydata.type="file",
      cormatrix.file=mycorrelation,  cormatrix.type="listfile",
      mydata.large.file=myexpressfile, mydata.large.type="listfile",
      tracks.gviz=listgviz, verbose=FALSE, print.image=FALSE)


## ----cometPlotmatrix, eval=FALSE, fig.keep='last'------------------------
## extdata <- system.file("extdata", package="coMET",mustWork=TRUE)
## configfile <- file.path(extdata, "config_cyp1b1_zoom_4comet.txt")
## myinfofile <- file.path(extdata, "cyp1b1_infofile.txt")
## myexpressfile <- file.path(extdata, "cyp1b1_infofile_exprGene_region.txt")
## mycorrelation <- file.path(extdata, "cyp1b1_res37_rawMatrix.txt")
## 
## chrom <- "chr2"
## start <- 38290160
## end <- 38303219
## gen <- "hg19"
## strand <- "*"
## 
## BROWSER.SESSION="UCSC"
## mySession <- browserSession(BROWSER.SESSION)
## genome(mySession) <- gen
## 
## genetrack <-genesENSEMBL(gen,chrom,start,end,showId=TRUE)
## snptrack <- snpBiomart(chrom, start, end, dataset="hsapiens_snp_som",showId=FALSE)
## iscatrack <-ISCATrack(gen,chrom,start,end,mySession, table="iscaPathogenic")
## 
## listgviz <- list(genetrack,snptrack,iscatrack)
## 
## matrix.dnamethylation <- read.delim(myinfofile, header=TRUE, sep="\t", as.is=TRUE,
##                                     blank.lines.skip = TRUE, fill=TRUE)
## matrix.expression <- read.delim(myexpressfile, header=TRUE, sep="\t", as.is=TRUE,
##                                 blank.lines.skip = TRUE, fill=TRUE)
## cormatrix.data.raw <- read.delim(mycorrelation, sep="\t", header=TRUE, as.is=TRUE,
##                                  blank.lines.skip = TRUE, fill=TRUE)
## 
## listmatrix.expression <- list(matrix.expression)
## listcormatrix.data.raw <- list(cormatrix.data.raw)
## comet(config.file=configfile, mydata.file=matrix.dnamethylation,
##       mydata.type="dataframe",cormatrix.file=listcormatrix.data.raw,
##       cormatrix.type="listdataframe",cormatrix.sig.level=0.05,
##       cormatrix.conf.level=0.05, cormatrix.adjust="BH",
##       mydata.large.file=listmatrix.expression, mydata.large.type="listdataframe",
##       tracks.gviz=listgviz,verbose=FALSE, print.image=FALSE)


## ----cometPlotMatrix, echo=FALSE, fig.keep='last'------------------------
extdata <- system.file("extdata", package="coMET",mustWork=TRUE)
configfile <- file.path(extdata, "config_cyp1b1_zoom_4comet.txt")
myinfofile <- file.path(extdata, "cyp1b1_infofile.txt")
myexpressfile <- file.path(extdata, "cyp1b1_infofile_exprGene_region.txt")
mycorrelation <- file.path(extdata, "cyp1b1_res37_rawMatrix.txt")

#configfile <- "../inst/extdata/config_cyp1b1_zoom_4comet.txt" 
chrom <- "chr2"
start <- 38290160
end <- 38303219
gen <- "hg19"
strand <- "*"

data(geneENSEMBLtrack)
data(snpBiomarttrack)
data(ISCAtrack)

listgviz <- list(genetrack,snptrack,iscatrack)

matrix.dnamethylation <- read.delim(myinfofile, header=TRUE, sep="\t", as.is=TRUE, blank.lines.skip = TRUE, fill=TRUE)
matrix.expression <- read.delim(myexpressfile, header=TRUE, sep="\t", as.is=TRUE, blank.lines.skip = TRUE, fill=TRUE)
cormatrix.data.raw <- read.delim(mycorrelation, sep="\t", header=TRUE, as.is=TRUE, blank.lines.skip = TRUE, fill=TRUE)

listmatrix.expression <- list(matrix.expression)
listcormatrix.data.raw <- list(cormatrix.data.raw)
comet(config.file=configfile, mydata.file=matrix.dnamethylation, 
      mydata.type="dataframe",cormatrix.file=listcormatrix.data.raw,
      cormatrix.type="listdataframe",cormatrix.sig.level=0.05,
      cormatrix.conf.level=0.05, cormatrix.adjust="BH",
      mydata.large.file=listmatrix.expression, mydata.large.type="listdataframe",
      tracks.gviz=listgviz,verbose=FALSE, print.image=FALSE)


## ----cometPlotNopvalText, eval=FALSE, fig.keep='last'--------------------
## extdata <- system.file("extdata", package="coMET",mustWork=TRUE)
## configfile <- file.path(extdata, "config_cyp1b1_zoom_4cometnopval.txt")
## myinfofile <- file.path(extdata, "cyp1b1_infofile.txt")
## mycorrelation <- file.path(extdata, "cyp1b1_res37_rawMatrix.txt")
## 
## chrom <- "chr2"
## start <- 38290160
## end <- 38303219
## gen <- "hg19"
## strand <- "*"
## 
## genetrack <-genesENSEMBL(gen,chrom,start,end,showId=FALSE)
## snptrack <- snpBiomart(chrom, start, end,
##                        dataset="hsapiens_snp_som",showId=FALSE)
## strutrack <- structureBiomart(chrom, start, end,
##                               strand, dataset="hsapiens_structvar_som")
## clinVariant<-ClinVarMainTrack(gen,chrom,start,end)
## clinCNV<-ClinVarCnvTrack(gen,chrom,start,end)
## gwastrack <-GWASTrack(gen,chrom,start,end)
## geneRtrack <-GeneReviewsTrack(gen,chrom,start,end)
## 
## listgviz <- list(genetrack,snptrack,strutrack,clinVariant,
##                  clinCNV,gwastrack,geneRtrack)
## comet(config.file=configfile, mydata.file=myinfofile, mydata.type="file",
##       cormatrix.file=mycorrelation, cormatrix.type="listfile",
##       tracks.gviz=listgviz, verbose=FALSE, print.image=FALSE,disp.pvalueplot=FALSE)


## ----cometPlot_nopval, echo=FALSE, fig.keep='last'-----------------------
extdata <- system.file("extdata", package="coMET",mustWork=TRUE)
configfile <- file.path(extdata, "config_cyp1b1_zoom_4cometnopval.txt")
#configfile <- "../inst/extdata/config_cyp1b1_zoom_4comet.txt" 
myinfofile <- file.path(extdata, "cyp1b1_infofile.txt")
mycorrelation <- file.path(extdata, "cyp1b1_res37_rawMatrix.txt")

chrom <- "chr2"
start <- 38290160
end <- 38303219
gen <- "hg19"
strand <- "*"

data(geneENSEMBLtrack)
data(snpBiomarttrack)
data(strucBiomarttrack)
data(ClinVarCnvTrack)
data(clinVarMaintrack)
data(GWASTrack)
data(GeneReviewTrack)

listgviz <- list(genetrack,snptrack,strutrack,clinVariant,
                 clinCNV,gwastrack,geneRtrack)
comet(config.file=configfile, mydata.file=myinfofile, mydata.type="file",
      cormatrix.file=mycorrelation, cormatrix.type="listfile",
      tracks.gviz=listgviz, verbose=FALSE, print.image=FALSE,disp.pvalueplot=FALSE)


## ----cometlist-----------------------------------------------------------
extdata <- system.file("extdata", package="coMET",mustWork=TRUE)
mycorrelation <- file.path(extdata, "cyp1b1_res37_rawMatrix.txt")
myoutput <- file.path(extdata, "cyp1b1_res37_cormatrix_list_BH05.txt")


comet.list(cormatrix.file=mycorrelation,cormatrix.method = "spearman",
           cormatrix.format= "raw", cormatrix.conf.level=0.05,
           cormatrix.sig.level= 0.05, cormatrix.adjust="BH",
           cormatrix.type = "listfile", cormatrix.output=myoutput, 
           verbose=FALSE)

listcorr <- read.csv(myoutput, header = TRUE,
                     sep = "\t", quote = "")
dim(listcorr)
head(listcorr)


## ----session-info, results="asis"----------------------------------------
toLatex(sessionInfo())