#' gather alignment statistic on a directory of star alignments
#'
#' @param projName project names
#' @param fileList list of log files
#' @param locDir location for (temporary) local storage of log files
#'
#' @export
summariseSTAR <- function(projName,fileList,localDir=T){
ret <- lapply(fileList,function(fn){
if(!localDir){
tmpFile <- plib::getFiles(filenames=fn,projName=projName)
}else{
tmpFile <- fn
}
res <- read.delim(tmpFile,sep="\t",head=F,row.names=1,stringsAsFactors=F)
rownames(res) <- gsub("[%]","Percent",gsub("[|]","",gdata::trim(rownames(res))))
rownames(res) <- gdata::trim(gsub("[|]","",rownames(res)))
rownames(res) <- gsub(" ","_",rownames(res))
t(res)
})
names(ret) <- gsub("Log[.]final[.]out$","",basename(fileList))
ret <- plyr::ldply(ret)
rownames(ret) <- make.names(ret[,1],unique=T)
ret[,-1]
}
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