Question: Apply Idr On List Of Read Counts
1
gravatar for 14134125465346445
6.8 years ago by
United Kingdom
141341254653464453.5k wrote:

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

----------------
GENERAL USAGE:
----------------
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?

R chip-seq statistics • 1.5k views
ADD COMMENTlink modified 6.7 years ago by Ying W3.9k • written 6.8 years ago by 141341254653464453.5k

may be this can help Irreproducible Discovery Rate and http://cran.r-project.org/web/packages/idr/idr.pdf

ADD REPLYlink modified 6.8 years ago by Istvan Albert ♦♦ 81k • written 6.8 years ago by Gjain5.4k
0
gravatar for Ying W
6.7 years ago by
Ying W3.9k
South San Francisco, CA
Ying W3.9k wrote:

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.

ADD COMMENTlink written 6.7 years ago by Ying W3.9k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1716 users visited in the last hour