On Wed, Jun 13, 2012 at 6:46 AM, Valerie Obenchain <vobencha@fhcrc.org>wrote:

> 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.
>
>
Although transcriptLocsToRefLocs would come really close. We would just
have to adjust for the translation start.


> 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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> >
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>
>

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