[Bioc-devel] Hunting for the subset generic definition?

[Hervé Pagès]

Done in BiocGenerics 0.15.4.

H.

On 07/29/2015 11:00 AM, Hervé Pagès wrote:
> Hi Steve,
>
> On 07/29/2015 10:40 AM, Steve Lianoglou wrote:
>> Hi folks,
>>
>> I'm looking to define a `subset` method on an S4 class of mine, but
>> can't find where to import the generic from.
>
> That's because subset() is an implicit generic, that is, there is no
> setGeneric statement for it, only setMethod statements. And so it's
> automatically turned into a generic the first time a package with
> a setMethod statement is loaded. More precisely, everything happens
> as if setGeneric("subset") was called right before the first time
> setMethod("subset", ...) is called.
>
>>
>> I can't seem to find it anywhere in:
>>
>>    * BiocGenerics
>>    * S4Vectors
>>    * XVector (
>>
>> Even though S4Vectors has a:
>>
>>    setMethod("subset", "DataTable", ...)
>>
>> It's not clear to me where it pulled the appropriate
>> `setGeneric("subset", ...)` from.
>
> I believe that you need to import it from S4Vectors. But things are
> going to be much clearer/cleaner if we make subset() an explicit
> generic by adding setGeneric("subset") to BiocGenerics. Which I'm
> going to do right now. Then you'll be able to import the subset()
> generic from BiocGenerics.
>
> Cheers,
> H.
>
>>
>> Can anyone provide a pointer?
>>
>> Thanks,
>> -steve
>>
>

-- 
Hervé Pagès

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