[Bioc-devel] need for consistent coordinate mapping API
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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