[BioC] get genomic location

[Valerie Obenchain]

Hi Mali,

Unfortunately we don't have a function that converts from protein-based
to genomic-based coordinates -  at least I'm unaware of one. The
conversion functions we do have are transcriptLocsToRefLocs() in
GenomicFeatures and refLocsToLocalLocs() in VariantAnnotation. The first
converts from transcript-based to genome-based and the second from
genome-based to transcript and protein-based.

Michael and I have plans to consolidate these coordinate-mapping
functions into the single 'Map' generic in IRanges. This will likely be
done for the next BioC release.

Valerie



On 06/12/2012 02:29 AM, mali salmon wrote:
> Hello List
> I have a basic question.
> Is there an easy way to convert a location in protein and mRNA to genomic
> location? (except of alignment...)
> For example, I have a list of point mutations in amino acids positions
> and/or positions in mRNA, and I would like to get their genomic locations.
> Thanks
> Mali
>
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