[BioC] extract introns

[Steve Lianoglou]

Hi,

On Tue, Nov 15, 2011 at 12:19 PM, Yating Cheng <yating.cheng at charite.de> wrote:
> Hi,
>
> I checked the function"gaps". But I am not sure how to use it. Is someone
> know how to use it to get the positions of introns?

Imagine a simple gene with two exons defined by these regions:

R> (exons <- GRanges('chr1', IRanges(c(10, 100), width=21), '+'))
GRanges with 2 ranges and 0 elementMetadata values:
      seqnames     ranges strand
         <Rle>  <IRanges>  <Rle>
  [1]     chr1 [ 10,  30]      +
  [2]     chr1 [100, 120]      +

Look for its introns here:

R> gaps(exons)
GRanges with 2 ranges and 0 elementMetadata values:
      seqnames    ranges strand
         <Rle> <IRanges>  <Rle>
  [1]     chr1  [ 1,  9]      +
  [2]     chr1  [31, 99]      +

In this case, you will have to remove the [1,9] range (maybe that's
intergenic region), which you can do with over fun interval operations
-- perhaps you can subsetByOverlaps the ranges returned from `gaps`
with the transcription start and end of your gene.

Or, if you're working w/ a GenomicFeatures TranscriptDb, there is
always the `intronsByTranscript` method ...

HTH,
-steve

-- 
Steve Lianoglou
Graduate Student: Computational Systems Biology
 | Memorial Sloan-Kettering Cancer Center
 | Weill Medical College of Cornell University
Contact Info: http://cbio.mskcc.org/~lianos/contact