[BioC] extract introns

[Steve Lianoglou]

Hi Yating,

Brief note: when replying to emails form the bioconductor list, make
sure to use "reply all" so the list is cc'd, this way others can
benefit from the help but also they can jump in to help in better
ways.

Ok, so:

On Thu, Nov 10, 2011 at 5:16 PM, Yating Cheng <yating.cheng at charite.de> wrote:
> Hi Steve
>
> Thanks very much for your answer. I am really a new hand in bioinfo.
>
> Actually now I have problem to create the GRanges object. The genes are
> from Apis mellifera.The data I have is like:
> "ensembl_gene_id" "chromosome_name" "exon_chrom_start" "exon_chrom_end"
> "strand"
> "1" "GB17244" "Group5.28" 95590 95776 1
> "2" "GB17244" "Group5.28" 95865 96055 1
> "3" "GB17244" "Group5.28" 96189 96428 1
> "4" "GB17244" "Group5.28" 100525 100632 1
> "5" "GB17244" "Group5.28" 100689 100751 1
> "6" "GB17244" "Group5.28" 100835 101145 1
> "7" "GB17244" "Group5.28" 101265 101547 1
> "8" "GB17244" "Group5.28" 101632 101673 1
> "9" "GB12201" "Group13.1" 374539 374712 -1
> "10" "GB12201" "Group13.1" 366611 366778 -1
> "11" "GB12201" "Group13.1" 366400 366513 -1
> "12" "GB12201" "Group13.1" 366115 366201 -1
> "13" "GB16402" "GroupUn.2" 208099 208254 1
> Do you know how to convert it into GRanges object.

Interesting names from chromosomes ... are they really "GBXXXX"?

Anyway, assuming they are, this is how you can convert that table into
a GRanges object. Let's assume the table you listed above is in a
data.frame called `xcripts`

R> gr.exons <- with(xcripts, {
  GRanges(chromosome_name,
    IRanges(exon_chrom_start, exon_chrom_end),
    ifelse(strand == 1, '+', '-'))
})

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