Question: Genomic overlap using ChIPseeker enrichPeakOverlap
0
gravatar for s-root
3.9 years ago by
s-root0
s-root0 wrote:

I am using ChIPseeker R package for finding overlaps between different datasets. The enrichPeakOverlap function gives me the overlap summary at the genomic co-ordinate level, and I was wondering if it is possible to get the actual co-ordinates where overlap is observed. For example, my output is:

qSample tSample qLen    tLen    N_OL    pvalue  p.adjust

peaks1  peaks2  1519    835 41  0.005988024 0.015968064

peaks1  peaks4  1519    301 12  0.005988024 0.015968064

qSample= query bed file(peaks1), tSample= target bed files(peaks 2, and 4), qLen= # of peaks in query, tLen= # of peaks in target, N_OL= # of overlapping peaks

Is it possible to get the genomic coordinates of the 41, and 12 overlapping regions using this tool? Any input would be helpful.

Thanks!

chipseeker chip-seq R • 1.7k views
ADD COMMENTlink modified 3.9 years ago by Guangchuang Yu2.4k • written 3.9 years ago by s-root0

Can't answer this but how does ChIPseeker compare to ChIPpeakAnno?

ADD REPLYlink written 3.9 years ago by YaGalbi1.5k

It's better in my personal opinion.

ADD REPLYlink written 3.9 years ago by Sinji3.1k

in what way? What is the benefit of switching to ChIPseeker?

ADD REPLYlink written 3.9 years ago by YaGalbi1.5k
0
gravatar for Guangchuang Yu
3.9 years ago by
Guangchuang Yu2.4k
China/Guangzhou/Southern Medical University
Guangchuang Yu2.4k wrote:

intersect(peaks1, peaks2) will give you the overlap.

ADD COMMENTlink written 3.9 years ago by Guangchuang Yu2.4k

Hello, I have a question about this: I have a similar output as above, with my N_OTL as 153.

peak1.bed peak2.bed 1530 82119 153 0.01398601 0.01398601

when I perform intersect(peaks1,peaks2) it gives me character(0). Any idea why that might be?

ADD REPLYlink written 3.4 years ago by lauren_wasson0
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