Dear Sukhdeep,

Thanks for the nice feedback and great suggestion! I have added minoverlap with default 1 bp to both findOverlappingPeaks and makeVennDiagram for the dev version with revision 65860.

For a diagram generated from two datasets A and B, there are 4 numbers, i.e., nA: number of peaks unique to A, nB: number of peaks unique to B, nAB: number of peaks shared in A and B, totalTest – nA – nB – nAB.

Best regards,

Julie


On 5/11/12 8:06 PM, "Sukhdeep Singh" <sukhdeepsingh.bio@gmail.com> wrote:

Hello Dr.Zhu.
I tried using ChIPPeakAnno, its really nice, just I am stuck in small thing.

When I used findOverlappingPeaks or makeVennDiagram direclty, is there any parameter for specifying the minimum overlap between the peaks of two chip-seq profiles as being implement in the intersectBed of the Bedtools (-f paramter - 0.5 specifies 50-100% overlap is an overlap)and supposedly opposite to the maxgap. Logically, maxgap should also be able to take a -ve values so as to define the same thing, but may there's a custom code or already implemented technique.

Also, when I make Venn Diagrams using the function I wrote above, what is the -ve number (0 by 0 case of 2 datasets) in the venn diagram on the right bottom.

Thanks a lot,

Sukhdeep Singh
Dresden



	[[alternative HTML version deleted]]

