Genomic overlap using ChIPseeker enrichPeakOverlap

Question

[s-root]

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!

[BioinfGuru]

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

[Sinji]

It's better in my personal opinion.

[BioinfGuru]

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

Answer 1

[Guangchuang Yu]

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

[lauren_wasson]

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?