p value of significance for overlapping peaks

Question

[qudrat.nii]

Hi all,

I have MACS2 peaks for two different transcription factors and I want to find the p-value for the significance peak overlapped between these two transcription factors. I can do a hypergeometric test to find the p-value but I do not know how to proceed. Please help me with some example.

Thank you

Answer 1

[i.sudbery]

We use the GAT tool for this. I believe there is an R package that does something similar (shuffles one set of peaks and then compares the overlap after shuffling), although I can't bring its name to mind now.