Get ChIPpeakAnno to report total number of covered bases in VennDiagrams instead of (or in addition to) regions
5
0
Entering edit mode
Brad Davis ▴ 20
@brad-davis-5385
Last seen 6.6 years ago
Canada

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 

chippeakanno • 683 views
ADD COMMENT
0
Entering edit mode
Julie Zhu ★ 4.3k
@julie-zhu-3596
Last seen 9 weeks ago
United States

Brad,

 

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

Best regards,

Julie

 

 

 

 

ADD COMMENT
0
Entering edit mode
Brad Davis ▴ 20
@brad-davis-5385
Last seen 6.6 years ago
Canada

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. 

 

ADD COMMENT
0
Entering edit mode
Julie Zhu ★ 4.3k
@julie-zhu-3596
Last seen 9 weeks ago
United States

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

ADD COMMENT
0
Entering edit mode
Brad Davis ▴ 20
@brad-davis-5385
Last seen 6.6 years ago
Canada

That would be perfect.

ADD COMMENT
0
Entering edit mode
Ou, Jianhong ★ 1.2k
@ou-jianhong-4539
Last seen 9 weeks ago
United States

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

ADD COMMENT

Login before adding your answer.

Traffic: 315 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6