qteller.2.matrix <-
function (cuffdiff.file , template.matrix.file , b73=FALSE){
library(tools)
matsuffix<-get.suffix(basename(template.matrix.file),"_")
winsize=as.numeric(gsub("mat","",file_ext(template.matrix.file)))
mat<-read.mat(template.matrix.file)
cuf<-read.csv(cuffdiff.file,header=T)
matgenes<-unlist(lapply(strsplit(row.names(mat),";") , "[" , 3 ))
if(b73){
matgenes<-remove.suffix(matgenes,"_T")
matgenes<-gsub("_FGT","_FG",matgenes)
}
namematch<-match(matgenes,cuf[,1])
for(i in 6:(ncol(cuf)-1 ) ) {
samplename<-colnames(cuf)[i]
outname <- paste0 (samplename,"_FPKM_",matsuffix)
m1<-matrix(as.numeric(cuf[namematch,i]),nrow=nrow(mat),ncol=ncol(mat))
row.names(m1)<-row.names(mat)
write.mat(m1,file=outname)
}
}
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