[Bioc-devel] adding methods to BiocGenerics
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@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
Re: [Bioc-devel] adding methods to BiocGenerics
On 19 May 2017 15:39, Stephanie M. Gogarten wrote:
> Dear Core Team,
>
> What do you think about adding the following generics to BiocGenerics?
>
> colData
> rowRanges
> ref
> alt
> qual
Currently exists in MSnbase with signature
setGeneric("qual", function(object) standardGeneric("qual"))
As far as I know, only used in that packages. I'm more than happy to use
BiocGenerics::qual when/if it becomes available.
> filt
> header
Currently exists in mzR with signature
setGeneric("header", function(object, scans, ...) standardGeneric("header"))
and is used at least in mzR and MSnbase.
I guess that signature, as it is, wouldn't be a good for BiocGenerics.
Best wishes,
Laurent
> 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
>
> ___
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--
Laurent Gatto | @lgatt0
http://cpu.sysbiol.cam.ac.uk/
http://lgatto.github.io/
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Re: [Bioc-devel] adding methods to BiocGenerics
Since SeqArray already imports SummarizedExperiment and VariantAnnotation, why can't it just move them to Depends and use their generics? On Fri, May 19, 2017 at 8:39 AM, Stephanie M. Gogarten 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@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/bioc-devel ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
Re: [Bioc-devel] adding methods to BiocGenerics
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)?
Martin
On Fri, May 19, 2017 at 8:39 AM, Stephanie M. Gogarten
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
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Re: [Bioc-devel] adding methods to BiocGenerics
That could work, also.
On Fri, May 19, 2017 at 10:27 AM, Martin Morgan
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)?
>
> Martin
>
>>
>> On Fri, May 19, 2017 at 8:39 AM, Stephanie M. Gogarten
>> 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@r-project.org mailing list
>>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>>
>>
>> ___
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>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>>
>
>
> This email message may contain legally privileged and/or...{{dropped:2}}
>
>
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Re: [Bioc-devel] adding methods to BiocGenerics
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
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
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
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