[BioC] IRanges problem: findOverlaps

[Nicolas DESCOSTES]

Thanks all for your reply. Just tried ChIPpeakAnno, it is doing well.

Cheers.



-----Original Message-----
From: Tim Triche, Jr. [mailto:tim.triche at gmail.com] 
Sent: Tuesday, July 10, 2012 6:47 PM
To: Jonathan Cairns
Cc: Nicolas DESCOSTES; bioconductor at r-project.org
Subject: Re: [BioC] IRanges problem: findOverlaps

how about

resize(genes,1, fix='start')
findOverlaps(peaks, genes)

however,

+1 for Julie Zhu's ChIPpeakAnno package since, as was just pointed
out, it is meant for such things!




On Tue, Jul 10, 2012 at 9:43 AM, Jonathan Cairns <Jonathan.Cairns at cancer.org.uk> wrote:
> 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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A model is a lie that helps you see the truth.

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