[Bioc-devel] Listing package-specific methods

[Michael Love]

This seems like a pretty simple solution, so I like that :)

On Mon, Jun 27, 2016 at 10:46 AM, Hervé Pagès <hpages at fredhutch.org> wrote:

> Hi Mike,
>
> IIUC you want to do something like
>
>   setdiff(methods(class="DESeqDataSet"),
>           methods(class="RangedSummarizedExperiment"))
>
> Maybe this could be handled by methods() itself e.g. with
> an extra argument that lets the user choose if s/he wants to see
> all the methods (i.e. specific + inherited) or only the specific
> ones?
>
> H.
>
> On 06/27/2016 09:39 AM, Michael Love wrote:
>
>> hi,
>>
>> Following on a conversation from Bioc2016, I think it would be good to
>> have
>> a function available to Bioconductor users that helps in the following
>> situation:
>>
>> I'm a user, trying out a new package 'foo', which defines the FooData
>> class, that builds on top of SummarizedExperiment. The package author has
>> defined a set of methods for the FooData class in the 'foo' package. From
>> the R console, I want to see a list of these methods, but I don't want to
>> look through the entire list of methods defined for SummarizedExperiment,
>> Vector, and Annotated.
>>
>> I think such a function should live somewhere easily accessible for
>> Bioconductor users. I worked out two implementations of this function
>> which
>> you can see here:
>>
>> http://rpubs.com/mikelove/pkgmethods
>>
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>>
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>>
>>
> --
> Hervé Pagès
>
> Program in Computational Biology
> Division of Public Health Sciences
> Fred Hutchinson Cancer Research Center
> 1100 Fairview Ave. N, M1-B514
> P.O. Box 19024
> Seattle, WA 98109-1024
>
> E-mail: hpages at fredhutch.org
> Phone:  (206) 667-5791
> Fax:    (206) 667-1319
>

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