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> 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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