[Bioc-devel] adding methods to BiocGenerics

[Stephanie M. Gogarten]

On 5/19/17 12:15 PM, Michael Lawrence wrote:
> That could work, also.
>
> On Fri, May 19, 2017 at 10:27 AM, Martin Morgan
> <martin.morgan at roswellpark.org> wrote:
>> On 05/19/2017 12:14 PM, Michael Lawrence wrote:
>>>
>>> Since SeqArray already imports SummarizedExperiment and
>>> VariantAnnotation, why can't it just move them to Depends and use
>>> their generics?
>>
>>
>> do they need to be moved to Depends? Or simply import the generic export the
>> new method(s) (and generic)?

We used to do this, but Xiuwen just moved SummarizedExperiment and 
VariantAnnotation from Imports to Suggests, because it was taking too 
long to load the package with them attached. So now we are redefining 
the generics.

In our daily use of SeqArray we almost never use VariantAnnotation or 
these generics, so the change improves our pipeline performance without 
any immediate downsides for us. But it does add annoyance for any 
(potential) users of both SeqArray and VariantAnnotation in the same 
session, as they would have to add the package name with "::" to 
disambiguate the methods.

>>
>> Martin
>>
>>>
>>> On Fri, May 19, 2017 at 8:39 AM, Stephanie M. Gogarten
>>> <sdmorris at u.washington.edu> wrote:
>>>>
>>>> Dear Core Team,
>>>>
>>>> What do you think about adding the following generics to BiocGenerics?
>>>>
>>>> colData
>>>> rowRanges
>>>> ref
>>>> alt
>>>> qual
>>>> filt
>>>> header
>>>> fixed
>>>> info
>>>> geno
>>>>
>>>> They are currently defined by both VariantAnnotation/SummarizedExperiment
>>>> and SeqArray. Given the increasingly widespread use of VCF files, it
>>>> seems
>>>> likely that other packages may want to use them in future also.
>>>>
>>>> Stephanie
>>>>
>>>> _______________________________________________
>>>> Bioc-devel at r-project.org mailing list
>>>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>>>
>>>
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>>
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