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List:       bioconductor
Subject:    Re: [BioC] ChIP-seq peaks in the vicinity of refseq exons
From:       Sean Davis <sdavis2 () mail ! nih ! gov>
Date:       2012-01-31 18:00:56
Message-ID: CANeAVB=RJ4H-5NnAhAB1hB3A35TdLeF054tB-3zj8YMg-yQVEA () mail ! gmail ! com
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Hi, Kavitha.

See the GenomicFeatures package, for example.  You will probably want
to get familiar with the GenomicRanges package, as well.

Sean


On Tue, Jan 31, 2012 at 12:57 PM, Kavitha Mukund <kmukund@ucsd.edu> wrote:
> Hello,
> 
> I have a list of ChIP seq- CTCF binding peaks for mouse. I was wondering what would \
> be the best way to identify if any peaks lie within 1000 bps upstream or downstream \
> of known exons (obtained from the ref seq table, ucsc genome browser). Is there a \
> library in R which lets me import the exon positions directly into R? 
> Thanks in advance,
> Kavitha
> 
> [[alternative HTML version deleted]]
> 
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