Entering edit mode
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
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