OLwithSI in peakEnrichment4Features

[Former user]

For testing purposes of peakEnrichment4Features, I called 439,542 interactions with Chicago and extracted from the .ibed: 1. only unique captured ends (33,736) 2. all other ends (non-captured) (298,059) and submitted them to analysis by peakEnrichment4Features with the 439,542 interactions .ibed.

To my surprise, OLwithSI was not 100% for either feature. It was: 1. 3,791 2. 228,772

feature OLwithSI MeanOLwithSamples SDOLwithSample LowerCI HigherCI fold.difference captured.bed 3791 2192.51 38.5941051132806 2116.86555397797 2268.15444602203 1.72906851051991 distal.bed 228772 59331.77 185.226634590213 58968.7257962032 59694.8142037968 3.85580945924924

I thought OLwithSI were the number of overlaps with the features being tested. Why aren't these numbers 100% of the overlaps? Thank you.