#!/usr/bin/env Rscript
args = commandArgs(trailingOnly=TRUE)
# test if there is at least one argument: if not, return an error
if (length(args)==0) {
stop("At least one argument must be supplied (input file).n", call.=FALSE)
} else if (length(args)>1) {
input.file.dir=args[1]
out.file.dir=args[2]
genome=args[3]
}
cat(input.file.dir,"\t",out.file.dir,"\t",genome,"\n")
library(ChipSeq)
PeakCallAndAnnotation(input.file.dir,out.file.dir,genome)
#BamFileSortIndexVisualization(input.file.dir,out.file.dir,genome)
#AnnotatePeak(paste0(temp3,"/"),"*macs142_peaks.bed",7,paste0(output.dir.name,"PeakAnnotation_at_",temp2),genome="Hs")
#SortBamFile(input.file.dir,input.file.pattern,as.numeric(index.file),out.file.dir,genome)
#re.from.bed.peng.4.venn<-ParserBamFile4NgsPlot(dir.name,as.numeric(index),input.file.pattern,out.dir.name,outfile)
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