I'm facing the following problem:
When using findOverlapsOfPeaks() with four Peak-Datasets and maxgap = 1000 I get 17376 peaks, which overlap in all four datasets when I look into the data. When using makeVennDiagram() to draw an image of the overlaps it says 18703 for all four datasets, which is kinda odd because I use the same data.
Here's what I did:
ol <- findOverlapsOfPeaks(peaks1, peaks2, peaks3, peaks4, maxgap=1000) peaklist <- ol$peaklist peaklist[["peaks1///peaks2///peaks3///peaks4"]] ## results into: GRanges object with 17376 ranges and 1 metadata column: makeVennDiagram(ol, totalTest=72033) ## says: 18703 for all sets overlapping
Any ideas what's the problem?
I am using ChIPpeakAnno_3.2.2