#' collate a directory of STAR .ReadsPerGene.out.tab files
#'
#' @param dirname directory name
#'
#' @export
collateRPG <- function(directoryName,projName,strandedness="US",force=F,loc=T){
if(!loc){
files <- rlsFiles(file.path(directoryName,"*ReadsPerGene.out.tab"))
}else{
files <- list.files(directoryName,pattern=".*ReadsPerGene.out.tab",full=T)
}
countList <- lapply(files,function(fn){
if(!loc){
tmpFile <- plib::getFiles(filenames=fn,projName=projName)
}else{
tmpFile <- fn
}
tab <- read.delim(tmpFile,sep="\t",head=F,row.names=1)
colnames(tab) <- c("US","FS","SS")
ret <- tab[,strandedness]
names(ret) <- rownames(tab)
ret
})
names(countList) <- gsub("ReadsPerGene.*$","",basename(files))
retMat <- plyr::ldply(countList)
rownames(retMat) <- retMat[,1]
t(retMat[,-1])
}
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