[BioC] extract introns

[Yating Cheng]

Hi, steve

Thanks for your answer. About converting the names of chromosome, it is
kind of difficult.

I need the intron sequences for every gene, but the chromosome names of
some genes I got from biomart are the same.

I am not sure about how can I get specific genes from BS genome, and match
them to gene-IDs.

Thanks .

Yating


> 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
>