#' fix scaffold file (utility function)
#' @param filename filename of scaffod quant reprot
#' @export
#'
fixScaffoldQuantReport <- function(filename){
scftab <- utils::read.csv(filename,sep="\t", stringsAsFactors = FALSE,skip=2)
scftab <- scftab[-nrow(scftab),]
tmp <- colnames(scftab)[2:ncol(scftab)]
scftab <- scftab[,-ncol(scftab)]
colnames(scftab) <- tmp
ACC<-gsub(" \\(\\+[0-9]+\\)$","",scftab$Accession.Number)
ACC<-gsub(" \\[[0-9]\\]$","",ACC)
rownames(scftab) <- ACC
return(scftab)
}
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