[BioC] IRanges problem: findOverlaps

[Jonathan Cairns]

Hi,

>From ?findOverlaps:

"If ‘type’ is ‘start’ or ‘end’, the intervals are required to have matching starts or ends, respectively."

This doesn't sound like it's what you're after, as type = "start" considers only the starts of peaks, as well as the starts of whatever annotation you're using.

Have you looked at the package ChIPpeakAnno? It is designed for annotating ChIP-seq peaks and might be useful.

Jonathan

________________________________________
From: bioconductor-bounces at r-project.org [bioconductor-bounces at r-project.org] On Behalf Of Nicolas DESCOSTES [descostes at ciml.univ-mrs.fr]
Sent: 10 July 2012 16:40
To: bioconductor at r-project.org
Subject: [BioC] IRanges problem: findOverlaps

Dear members,

I have a set of chip-Seq peaks which I want to find the overlap with a bench of annotations downloaded from ucsc.

When I am doing the overlap between my peaks and annotations list, I am finding 5635 positive matches. When adding "type = "start"", I have no results returned. However, when I am visualizing the 5635 intervals, it overlaps many start site of my genes annotations.

I tried to update IRanges but I am still getting no results.

Any idea?

Thanks.


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