[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:
>> Hi,
>> I'm implementing a few things in oligo and I wonder if it'd make sense to have
>> boxplot/coef/image/ncol/residuals
>> defined in BiocGenerics?
>> If it's only me using them, I'm happy to have everything in oligo.
>> Thoughts?
> 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?
> Sean
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