[Bioc-devel] need for consistent coordinate mapping API

Hervé Pagès hpages at fhcrc.org
Fri Sep 19 21:00:32 CEST 2014


It's an interesting problem. Right now mapCoords() has some
limitations. For example I can use it to map from reference sequence
to read cycle but not the other way around. Or from reference genome
to transcriptome but not the other way around (this reverse mapping
is actually what low level util transcriptLocs2RefLocs() does).
Ideally we should be able to easily go back and forth between 2
coordinate spaces.

Also we need to think about how more complex use cases (like Laurent's
one) could be handled by mapCoords(). Not clear. We might need to
change mapCoords's design a little bit, or maybe we'll need something


On 09/19/2014 10:40 AM, Laurent Gatto wrote:
> On 19 September 2014 18:07, Michael Lawrence wrote:
>> Hi guys,
>> This is the problem of mapping back and forth between coordinate spaces,
>> such as between genomic and transcript space. I think there was some
>> progress this release cycle (introduction of mapCoords generic, etc), but I
>> think there is yet more to do. For example, transcriptLocs2RefLocs could be
>> given a ranges-based wrapper that conforms to the mapCoords API somehow.
>> Could we please put this on the TODO list of someone (in Seattle) for the
>> next release cycle?
> And I would be very interested in (and slowly working towards)
> generalising this to proteomics data. For now, there is a rather long
> description in [1], but eventually, it should be standardised. I was not
> aware of mapCoords and will read about it.
> Laurent
> [1] http://bioconductor.org/packages/devel/bioc/vignettes/Pbase/inst/doc/mapping.html
>> Michael
>> 	[[alternative HTML version deleted]]
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Hervé Pagès

Program in Computational Biology
Division of Public Health Sciences
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