Hi. I am trying to see whether the peaks in my TF ChIP-seq experiment overlap with the peaks of different epigenetic marks. However, it gave me the same p value even though the number of overlapped peaks were different.

I used the enrichPeakOverlap function as below:

H3K4me2 overlap test

enrichPeakOverlap(queryPeak = "IntersectH3K4me2.narrowPeak", targetPeak = "TargetChIP_peaks.narrowPeak", nShuffle=5000, TxDb = TxDb.Hsapiens.UCSC.hg38.knownGene , pAdjustMethod="BH", chainFile=NULL)

permutation test of peak overlap... 2020-07-26 03:56:44 PM |======================================================================| 100% qSample tSample qLen tLen NOL 1 IntersectH3K4me2.narrowPeak TargetChIPpeaks.narrowPeak 407400 15559 5535

pvalue p.adjust 1 0.00019996 0.00019996

H3K4me3 overlap test

enrichPeakOverlap(queryPeak = "IntersectH3K4me3.narrowPeak", targetPeak = "TargetChIP_peaks.narrowPeak", nShuffle=5000, TxDb = TxDb.Hsapiens.UCSC.hg38.knownGene , pAdjustMethod="BH", chainFile=NULL)

permutation test of peak overlap... 2020-07-26 03:56:44 PM |======================================================================| 100% qSample tSample qLen tLen NOL 1 IntersectH3K4me3.narrowPeak TargetChIPpeaks.narrowPeak 145835 15559 766

pvalue p.adjust 1 0.00019996 0.00019996

The values are the same for other overlapping other epigenetic marks with my Target peaks. It either said 0.00019996 or 1 I am wondering is it normal? Thanks.