[BioC] Mapping genomic coordinates to transcript coordinates?

[Hollis Wright]

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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