[Bioc-devel] need for consistent coordinate mapping API

Laurent Gatto lg390 at cam.ac.uk
Fri Sep 19 19:40:49 CEST 2014

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.


[1] http://bioconductor.org/packages/devel/bioc/vignettes/Pbase/inst/doc/mapping.html

> Michael
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