[Bioc-sig-seq] Why are there non-imformative names() from GenomicFeatures:::exonsBy(...)?

Hervé Pagès hpages at fhcrc.org
Thu Aug 19 09:50:58 CEST 2010

Hi Steve,

On 08/17/2010 02:37 PM, Steve Lianoglou wrote:
> Once we get our own R2D2 like 3d/hologram displays/projectors, perhaps
> revisiting this issue would be fruitful ... :-)


>>> Yes, that's what I'm asking -- I'd like functions like exonsBy, cdsBy,
>>> transcripts, exons, etc. to be S4-ized (and allowed to take an '...'
>>> parameter).
>> Sounds good to me. I'll wait a couple of days before I make the change
>> so people have time to comment/object if they want.
> Thank you.

All these functions are generic starting with GenomicFeatures
1.1.11 (devel only).

> ... the getMetadata(...) IMHO *is* actually more useful to the
> consumer of the package, though.

I added a "metadata" method for TranscriptDb objects to GenomicFeatures
1.1.11. Note that for naming getters / setters in R, the foo / foo<-
convention can be used.

I also added a man page for id2name() as discussed previously.

> The only reason I linked to that page github page, though, was that I
> thought it might be helpful to you if I gave you a list of functions I
> identified in the GenomicFeatures package that I trampled/S4-ized, not
> to tell you guys how to design your packages ... sorry if it came
> across that way :-)

No worries. Having feedback is always good.


Hervé Pagès

Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
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