There probably needs to be a feature in GenomicRanges that does this for a
GRangesList, considering splicing, etc. It wouldn't be that hard to
implement.

Any takers?

On Mon, Nov 29, 2010 at 3:11 PM, Marc Carlson <mcarlson@fhcrc.org> wrote:

> Hi Hollis,
>
> Have you looked at the GenomicFeatures package?  It should allow you to
> get annotations for transcripts from biomaRt or UCSC and then pull out
> GRangesList objects that represent the different transcripts for each
> gene mapped into genomic coordinates.  You could then compare that to
> your data using findOverlaps().
>
>
>  Marc
>
>
>
> On 11/29/2010 02:07 PM, Hollis Wright wrote:
> > Something similar to this is what I initially tried, yes. We'd like to do
> it for the spliced transcript, however, and that's where we are having the
> difficulty since the splice can move the reading frame.
> >
> > Hollis Wright, PhD
> > Oregon Clinical and Translational Research Institute
> > ________________________________________
> > From: Michael Lawrence [lawrence.michael@gene.com]
> > Sent: Monday, November 29, 2010 1:41 PM
> > To: Hollis Wright
> > Cc: bioconductor@r-project.org
> > Subject: Re: [BioC] Mapping genomic coordinates to transcript
> coordinates?
> >
> > Sounds like this would be relatively straight-forward: call
> IRanges::findOverlaps to find the transcript(s) for each polymorphism and
> then subtract the transcription start from the position (and add 1),
> remembering to flip the operation for the negative strand.
> >
> > I could see the "shift" function being used for this, where the 'shift'
> argument is a Ranges, using the starts. A GenomicRanges method could account
> for the strand, but "shift" does not yet dispatch on its second argument.
> But maybe there needs to be a new generic with a better name.
> >
> > On Mon, Nov 29, 2010 at 1:01 PM, Hollis Wright <wrighth@ohsu.edu<mailto:
> wrighth@ohsu.edu>> wrote:
> > Hi, all; is there an easy way/function to map genomic coordinates into
> coordinates in a given transcript? We've got a number of potential
> polymorphisms we've mapped into UCSC coordinates and we are trying to figure
> out their positions in associated transcripts so we can figure out the
> reading frame and extract the changes (if any) to coding, but I haven't
> found an easy way to do so in Bioconductor. This seems like the sort of
> thing someone would have a package for but I haven't been able to find it.
> Any thoughts?
> >
> > Hollis Wright, PhD
> > Oregon Clinical and Translational Research Institute
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