[Bioc-devel] Candidates for BiocGenerics
Kevin R. Coombes
kevin.r.coombes at gmail.com
Thu Mar 1 19:13:04 CET 2012
I think that everything that is already an S3 generic in R should be
(automatically) upgraded to an S4 generic. (Four out of five of
Benilton's suggestions already qualify by that criterion. And ncol
should clearly be promoted to a generic for Bioc usage.) And a
suggestion by even one person who is using any base R function as a
generic should easily be enough to get it included in BiocGenerics.
I think the only question is whether there should be a core place (like
BiocGenerics) to contain the definitions of generics that don't
replace/extend functions in base R. For example, I could imagine more
than one person wanting a "process" generic to handle some processing
step for some high-throughput platforms. Is there any procedure for
dealing with things like this?
On 3/1/2012 10:18 AM, Sean Davis wrote:
> On Thu, Mar 1, 2012 at 7:57 AM, Benilton Carvalho
> <beniltoncarvalho at gmail.com> wrote:
>> I'm implementing a few things in oligo and I wonder if it'd make sense to have
>> defined in BiocGenerics?
>> If it's only me using them, I'm happy to have everything in oligo.
> It seems that if someone is proposing a generic for functionality
> already in base R, that generic is by definition a good candidate for
> inclusion in BiocGenerics. Are there downsides to having this be a
> criterion for inclusion?
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