[BioC] find overlap of bed files of different length

[Martin Morgan]

On 01/29/2011 04:33 PM, Duke wrote:
> Hi all,
> 
> I need to find overlap between a text file (BED format) and a gene
> reference. The BED file contains sequence of different lengths, and I
> need to find all the sequences that lye inside the gene (meaning
> overlapping percentage is 100%). I found findOverlaps function in
> GenomicRanges, but the parameter to control overlap (minoverlap) does
> not let me control percentage.

the 'tyoe='within"' argument is available for
findOverlaps,IRanges,IRanges-method; you could use this by extracting
the ranges(gr) from your query / subject for each seqname / strand
subset you were interested in.

The development version of GenomicRanges also now supports
findOverlaps,GenomicRanges,GenomicRangaes-method, so using the
development version of R is also a solution.

Martin


> 
> Anybody has any suggestion for me?
> 
> Thanks so much,
> 
> D.
> 
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