I am seeking some tips on how to calculate the pearson/spearman correlation between two chip seq peak profiles. I have the coordinates of the peaks in a bed format.
I think I have to bin the peaks and correlate the read count in aligned bins but I'm wandering, how to make sure the correct bins are correlated to each other?
if two similar peaks (from the two replicate IPs) have fairly different start coordinates that are shifted by several kb, then its possible they will belong to different bins. So how to account for this in the correlation in order to make sure that your bins are properly aligned ?
Thanks a lot for your suggestions.