Hi all,

I was wondering if there is anyway to get ChIPpeakAnno to report the total number of covered bases (as opposed to the number of overlapping regions) when making use of makeVennDiagram()?  Is this possible? Would it be difficult to add this as a feature?

Thanks,
Brad 

Brad,

Could you please send us a toy example and the output you expect? Thanks!

Best regards,

Julie

In the example posted below, the numbers in each of the sections of the venn diagram represent the number of overlapping regions (correct?).  What I would like is to report the total amount of coverage in terms of the number of base pairs in each of those sets of regions. 

Thanks, Brad!

How about add another parameter overlapRegionOrBase = c("region", "base")? Please note that p-values will be different if chosen "base". 

Best regards,

Julie

That would be perfect.

Hi Brad,

The function is ready in develop version 2.17.2 (99046). Please try to set byBase as TRUE to get overlaps in nucleotide level.

If you want to ignore the strand information when calling makeVennDiagram, please remove the strand info from RangedData before call.

Thanks again for the suggestion.

Jianhong