[BioC] ChIPpeakAnno makeVennDiagram

[Binbin Liu]

Hello there,

At the moment, I use findOverlappingPeaks function to identified the overlapping peaks between two dataset A and B, and use makeVennDiagram to show the overlapping. However, I have find two problems

1) in findOverlappingPeaks function , multiple can be switched on to find multiple overlaps of B in A. However, there is no such option available in makeVennDiagram. This leads to inconsistent number of overlapping peaks output from findOverlappingPeaks and makeVennDaigram. How to solve this issue?

2) I also find that by swapping makeVennDiagram(RangedDataList(A, B), .....) and makeVennDiagram(RangedDataList(B, A), .....),  the number of overlapping peaks is different. Why does it happen? and what is the proper way to do use makeVennDiagram() function?


Thanks for any suggestions.

Regards,
Binbin