[BioC] Mapping genomic coordinates to transcript coordinates?

[Marc Carlson]

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 at gene.com]
> Sent: Monday, November 29, 2010 1:41 PM
> To: Hollis Wright
> Cc: bioconductor at 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 at ohsu.edu<mailto:wrighth at 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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