[BioC] Mapping genomic coordinates to transcript coordinates?

[Hollis Wright]

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