R/JavaInterface.R

In wzthu/esATAC: An Easy-to-use Systematic pipeline for ATACseq data analysis

.fseq_call <- function(bedFileList,background=NULL,genomicReadsCount=NULL,inputDir=NULL,
                       fragmentSize=NULL,featureLength=NULL,outputDir=NULL,
                       outputFormat=c("bed","wig","npf"), ploidyDir=NULL,
                       wiggleTrackStep=NULL,threshold=NULL,verbose=NULL,
                       wgThresholdSet=NULL){
  argvs<-as.character(bedFileList)
  if(!is.null(background)){
    argvs<-c(argvs,"-b",background)
  }
  if(!is.null(genomicReadsCount)){
    argvs<-c(argvs,"-c",genomicReadsCount)
  }
  if(!is.null(inputDir)){
    argvs<-c(argvs,"-d",inputDir)
  }
  if(!is.null(fragmentSize)){
    argvs<-c(argvs,"-f",fragmentSize)
  }
  if(!is.null(featureLength)){
    argvs<-c(argvs,"-l",featureLength)
  }
  if(!is.null(outputDir)){
    argvs<-c(argvs,"-o",outputDir)
  }
  if(!is.null(outputFormat)){
    argvs<-c(argvs,"-of",outputFormat[1])
  }
  if(!is.null(ploidyDir)){
    argvs<-c(argvs,"-p",ploidyDir)
  }
  if(!is.null(wiggleTrackStep)){
    argvs<-c(argvs,"-s",wiggleTrackStep)
  }
  if(!is.null(threshold)){
    argvs<-c(argvs,"-t",threshold)
  }
  if(!is.null(verbose)&&verbose){
    argvs<-c(argvs,"-v")
  }
  if(!is.null(wgThresholdSet)){
    argvs<-c(argvs,"-wg",wgThresholdSet)
  }
  invisible(fseq(argvs))

}