[Bioc-devel] Candidates for BiocGenerics

[Martin Morgan]

On 03/01/2012 10:20 AM, Hervé Pagès wrote:
> Hi Benilton, Sean,
>
> On 03/01/2012 08:18 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.
>
> I agree.
>
>> Are there downsides to having this be a
>> criterion for inclusion?
>
> Not that I know of.
>
> I'll add boxplot, coef, image, ncol and residuals to BiocGenerics today.
> I'll also add nrow, NROW, NCOL and dim, which are all interconnected
> with ncol.

I had not really been aware that 'stats4' plays the same kind of role, 
in a limited sense, in base R. So for these

 > grep("^[^.]", getNamespaceExports("stats4"), value=TRUE)
  [1] "AIC"     "BIC"     "coef"    "confint" "logLik"  "mle"     "nobs"
  [8] "plot"    "profile" "show"    "summary" "update"  "vcov"

one would like instead to Imports: stats and importFrom(stats, plot) 
etc. This means that recent changes to add plot and summary to 
BiocGenerics should be undone...

Martin

 >

>
> Cheers,
> H.
>
>>
>> Sean
>>
>> _______________________________________________
>> Bioc-devel at r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>
>


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