[BioC] Getting Introns Expression at a Per Gene Level

[Valerie Obenchain]

Hi Carl,

You can use import() from rtracklayer to read a bed in as a GRanges.

     gr <- import('myfile.bed', asRangedData=FALSE)

I'm not sure what you've got in your file but let's say they are gene 
isoforms. Presumably there is an identifier in the file that would let 
you group the ranges by gene (or whatever grouping you are after). This 
will likely end up as one of the metadata columns in the GRanges after 
import. Create a GRangesList by grouping the GRanges by gene.

     grl <- split(gr, bySomeFactor)

The introns are the gaps between the ranges in each list element of the 
GRangesList. To get at these we want the difference between the full 
range of the gene and the multiple elements (exons or transcripts etc.) 
of the gene.

Create the gene ranges:

     geneRanges <- range(grl)

Extract the differences:

     introns <- psetdiff(geneRanges, grl)


If this doesn't help, I'll need to know more detail about the data in 
the isoform file.

Valerie


On 09/09/2013 07:31 PM, Carl Baribault wrote:
> Dear Valerie,
> I have a bed file of specific isoforms of interest.  Can you please suggest
> a best approach for obtaining the intron extents?  Thanks.
>
> Best,
> Carl Baribault
>
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