[Bioc-devel] BiocGenerics proposal

Hervé Pagès hpages at fhcrc.org
Tue Mar 6 00:53:56 CET 2012

Hi Steve,

On 03/05/2012 03:43 PM, Steve Lianoglou wrote:
> 2012/3/5 Hervé Pagès<hpages at fhcrc.org>:
>> Hi,
>> Sure, I'm for having ... in as many generics as possible. I complained
>> a long time ago about this on R-devel (I needed the ... arg to rev(),
>> which was never added, so I created my own reverse() generic in
>> IRanges).
>> I'll add ... to strand and `strand<-`.
> Nice, thanks Hervé!
> Now, how about the matter of adding `counts(x, ...)` to BiocGenerics
> ... it's a good idea, yes? :-)

Yes of course, moving all the "count-related" generics used by DESeq
and DEXSeq from Biobase to BiocGenerics has been on my list for a
while. It's not just counts(): there are 12 of them! I want to do this
before the next release but didn't find the time to work on this yet.
Will try to find some time this week...


> Thanks,
> -steve

Hervé Pagès

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