[Bioc-devel] Candidates for BiocGenerics

Hervé Pagès hpages at fhcrc.org
Thu Mar 1 19:47:00 CET 2012

Hi Kevin,

On 03/01/2012 10:13 AM, Kevin R. Coombes wrote:
> 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?

No formal procedure but it could also be placed in BiocGenerics.

We already have things there (combine, updateObject) that don't
replace/extend functions in base R (see ?BiocGenerics).

I also have on my list to move all the generics for count datasets
currently defined in Biobase (and used by the DESeq and DEXSeq
packages) to BiocGenerics.

The criteria for such a move is not as clear as for the stuff that
is already in base R though. What we want to avoid is having the same
generic defined twice so if 2 packages want to define a "process"
generic then one should depend on the other one so the second one
does not need to redefine the generic, it just needs to define methods
on it. If, for whatever reason, having one package depend on the
other is not desirable, then the generic should go in BiocGenerics.


> Kevin
> 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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Hervé Pagès

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