[BioC] ChIPpeakAnno makeVennDiagram

Zhu, Lihua (Julie) Julie.Zhu at umassmed.edu
Mon Dec 6 17:39:24 CET 2010


Thank you very much for the feedback and great suggestions!

1) We could add multiple as a parameter in the makeVennDiagram function.
However, the significance test should not be based on multiple=yes since you
might count some peaks multiple times simply because one peak in one dataset
overlaps multiple peaks in another dataset.

2) When there are multiple peaks from one dataset (A) overlap with one peak
from the other dataset (B), the number of overlap will depend on the order
of the list RangedDataList(A, B) vs RangedDataList(B, A). I would suggest
use the smaller number resulted from the order RangedDataList(B, A). We
could implement this inside the function to make it more user friendly if
that is useful. 

Best regards,


On 12/6/10 10:15 AM, "Binbin Liu" <B.B.Liu at leeds.ac.uk> wrote:

> 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
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