R/PermutationOfRawData.R

In aiminy/PathwaySJ: A R package for GO term enrichment analysis with the flexible bias factor adjustment

#' Title
#'
#' @param dir.name
#' @param file.sample
#' @param file.count
#' @param file.gff
#'
#' @return
#' @export
#'
#' @examples
#'
#' dir.name="/Volumes/Bioinformatics$/2015/Nimer_Cheng/"
#' file.sample="decoder.bySample.txt"
#' file.count="_junction_seq_new_gtf_7/QC.spliceJunctionAndExonCounts.forJunctionSeq.txt"
#' file.gff="Mus_musculus.GRCm38.83.JunctionSeq.flat.gff"
#' Re<-PermutattionOfRawData(dir.name,file.sample,file.count,file.gff)
#'
PermutattionOfRawData<-function(dir.name,file.sample,file.count,file.gff){
  #Get sample file
  path.file.sample<-paste0(dir.name,file.sample)
  decoder.bySample<-read.table(path.file.sample,header=T,stringsAsFactors = F)

  print(decoder.bySample)

  #Get count file
  path.file.count<-paste0(dir.name,decoder.bySample$sample.ID,file.count)
  countFiles<-paste0(path.file.count)

  print(countFiles)

  #Get annotation file
  path.file.gff<-paste0(dir.name,file.gff)

  print(path.file.gff)

  #Analysis
#  jscs.2<-runJunctionSeqAnalyses(sample.files= countFiles,sample.names= decoder.bySample$sample.ID,condition= decoder.bySample$group.ID,
#                                 flat.gff.file=path.file.gff,nCores=1,verbose=TRUE,debug.mode=TRUE,use.multigene.aggregates = TRUE)

#  return(jscs.2)
}