Question: Different amount of overlapping Peaks in ChIPpeakAnno-Package
0
3.7 years ago by
N. F.0
Germany
N. F.0 wrote:

Hey guys,

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