[Bioc-devel] Making GenomicRanges::genome generic more generic ...

Hervé Pagès hpages at fhcrc.org
Sat Nov 5 00:21:02 CET 2011

Hi Steve,

On 11-11-04 02:02 PM, Steve Lianoglou wrote:
> Hi all,
> It looks like the `genome` generic function from rtracklayer has moved
> to GenomicRanges in the 2.9 release train, and subsequently lost its
> `...` param.

I moved it, together with the `genome<-` generic, and dropped the `...`
arg from `genome` because (1) I couldn't find any method in BioC
that uses this arg, (2) `genome` (getter) and `genome<-` (setter)
are aimed to be accessors and it's unusual to have `...` in an
accessor, (3) it was a little bit ackward to have `...` in the getter
but not in the setter.

> Would anybody mind if I add the `...` back to the genome function now
> defined in GenomicRanges? I'll be careful to update the setMethods
> where appropriate in GenomicRanges, but I guess other packages will
> also need to update (rtracklayer) that I can't commit to.

In devel? Sure. It's a perfect time to break things ;-) I'm not so sure
about release though. What other people think?

> I was `importFrom(rtracklayer, genome)`-ing the genome function in one
> of my packages ... switching it to importFrom GenomicRanges isn't a
> problem, but I use the `...`
> (here's another post that touches on the "need" for a centralized
> BiocGenerics (or whatever) package that pops up from time to time).

Not every generic is going to make it to BiocGenerics. Also a generic
function is not just a name, there are also some expectations about what
kind of operation its methods should do.


> Thanks,
> -steve

Hervé Pagès

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