There is a method on the map generic in GenomicRanges that will do this
given a GRanges of genomic/global coordinates, and a GRangesList defining
transcripts or any other type of compound region. The returned
RangesMapping object tells you the hits (which overlapped which) and for
each hit the local coordinates.

Michael


On Tue, Sep 17, 2013 at 9:33 AM, Tim Johnstone
<timothy.johnstone@yale.edu>wrote:

> To add to my previous email, I just found the refLocsToLocalLocs function
> in the VariantAnnotation package you co-authored, but need to convert
> single positions that align anywhere in the transcript, rather than ranges
> that align to just the coding region. It looks like it may be possible to
> get this behavior by supplying exonsByTx as both the second and the third
> arguments, but let me know if there is an easier way.
>
> Best,
> Tim Johnstone
>
>
> On Tue, Sep 17, 2013 at 12:19 PM, Tim Johnstone <
> timothy.johnstone@yale.edu> wrote:
>
>> Dear Michael,
>>
>> I am working with the GenomicRanges bioconductor package, and I've been
>> trying to find a way to convert a set of locations in genomic coordinates
>> to transcript coordinates. I found an old mailing list conversation<https://stat.ethz.ch/pipermail/bioconductor/attachments/20110316/01b4dc42/attachment.pl>in which you indicated you were planning to implement that function
>> (refLocs2TranscriptLocs or globalToLocal) in GenomicRanges/GenomicFeatures,
>> but in looking through the source code I can't find it. Was this function
>> ever implemented, and if so, would it be possible for you to send it to me?
>>
>> Thanks!
>> Tim Johnstone
>>
>> --
>> Timothy G. Johnstone <http://timothyjohnstone.com/>
>> Yale University School of Medicine
>> New Haven, CT 06510
>> 503-318-0962
>>
>
>
>
> --
> Timothy G. Johnstone
> Yale University School of Medicine
> New Haven, CT 06510
> 503-318-0962
>

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