[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 > > ___ > Bioc-devel@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/bioc-devel -- Laurent Gatto | @lgatt0 http://cpu.sysbiol.cam.ac.uk/ http://lgatto.github.io/ ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
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 ___ 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 This email message may contain legally privileged and/or...{{dropped:2}} ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
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 >> >> >> ___ >> Bioc-devel@r-project.org mailing list >> https://stat.ethz.ch/mailman/listinfo/bioc-devel >> > > > This email message may contain legally privileged and/or...{{dropped:2}} > > > ___ > 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 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 ___ 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 This email message may contain legally privileged and/or...{{dropped:2}} ___ 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