Genomic overlap using ChIPseeker enrichPeakOverlap
1
0
Entering edit mode
4.3 years ago
s-root • 0

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!

ChIP-Seq R ChIPseeker • 1.8k views
ADD COMMENT
0
Entering edit mode

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

ADD REPLY
0
Entering edit mode

It's better in my personal opinion.

ADD REPLY
0
Entering edit mode

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

ADD REPLY
0
Entering edit mode
4.3 years ago
Guangchuang Yu ★ 2.5k

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

ADD COMMENT
0
Entering edit mode

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 REPLY

Login before adding your answer.

Traffic: 2411 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6