Apply Idr On List Of Read Counts
Does anybody know how to apply the IDR code on lists of read counts per peak, instead of the usual narrowPeak format:
peak-1 20
peak-2 25
peak-3 23
...
So that using IDR and my peak counts, I get a threshold of the minimum peak intensity for my samples?
I suppose the best version to use is the one explained below, as seen on this url:
http://sites.google.com/site/anshulkundaje/projects/idr
(1) batch-consistency-analysis.r
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GENERAL USAGE:
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Rscript batch-consistency-analysis.r [peakfile1] [peakfile2] [peak.half.width] [outfile.prefix] [min.overlap.ratio] [is.broadpeak] [ranking.measure]
Typical usage for SPP peak caller peaks
Rscript batch-consistency-analysis.r [peakfile1] [peakfile2] -1 [outfile.prefix] 0 F q.value
Typical usage for MACSv2 peak caller peaks
Rscript batch-consistency-analysis.r [peakfile1] [peakfile2] -1 [outfile.prefix] 0 F p.value
[peakfile1] and [peakfile2] are the peak calls for the pair of replicates in narrowPeak format. They must be uncompressed files.
e.g. /peaks/reps/chipSampleRep1_VS_controlSampleRep0.narrowPeak AND /peaks/reps/chipSampleRep2_VS_controlSampleRep0.narrowPeak
Any ideas?
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1 answer
I think you need a bit more information to call IDR. It is possible to convert your file of peaks to to a narrowPeak-like format by adding artificial non-overlapping chromosome locations however I think IDR works best with SPP output. You could try posting to their google groups page, the author (Anshul) is pretty active on there.
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may be this can help Irreproducible Discovery Rate and http://cran.r-project.org/web/packages/idr/idr.pdf