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!