# pipe.ChIPseq.R
# do the A to Z alignment pipeline on a ChIPseq sample
`pipe.ChIPseq` <- function( sampleID=NULL, annotationFile="Annotation.txt", optionsFile="Options.txt",
...) {
checkSampleNames( sampleID)
target <- getAndSetTarget( optionsFile, verbose=T)
# note the time we start
startTime <- proc.time()
# setup...
ans0 <- pipe.PreAlignTasks( sampleID, annotationFile, optionsFile, dataType="ChIP-seq")
# do the alignment
ans1 <- pipe.ChIPalignment( sampleID, annotationFile, optionsFile)
# make pileups but not a transcriptome
ans2 <- pipe.AlignToWig( sampleID, annotationFile, optionsFile, dataType="ChIP-seq")
# do the peak picking...
ans3 <- pipe.ChIPpeaks( sampleID, annotationFile, optionsFile, ...)
# make any extra wanted display files
ans4 <- pipe.PostAlignTasks( sampleID, annotationFile, optionsFile, dataType="ChIP-seq")
# done... report total time used
cat( "\n", verboseOutputDivider, "\n\nChIP-seq PIPELINE DONE: ", sampleID, "\n\n")
print( elapsedProcTime( startTime, proc.time(), N=ans1$nReadsIn))
return()
}
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