[Bioc-devel] 'semantically rich' subsetting of SummarizedExperiments

[Sean Davis]

On Sat, Sep 20, 2014 at 3:11 PM, Gabe Becker <becker.gabe at gene.com> wrote:

> Hey all,
>
> We are in the (very) early stages of experimenting with something that
> seems relevant here: classed identifiers. We are using them for
> database/mart queries, but the same concept could be useful for the cases
> you're describing I think.
>
> E.g.
>
> > mysyms = GeneSymbol(c("BRAF", "BRCA1"))
> > mysyms
> An object of class "GeneSymbol"
> [1] "BRAF"  "BRCA1"
> > yourSE[mysyms, ]
> ...
>
>
This approach has the flavor of some of the functionality that Martin put
together for the GSEABase package (EntrezIdentifier, etc.).

Sean



>
> This approach has the benefit of being declarative instead of heuristic
> (people won't be able to accidentally invoke it), while still giving most
> of the convenience I believe you are looking for.
>
> The object classes inherit directly from character, so should "just work"
> most of the time, but as I said it's early days; lots more testing for
> functionality and usefulness is needed.
>
> ~G
>
>
> On Sat, Sep 20, 2014 at 11:38 AM, Vincent Carey <
> stvjc at channing.harvard.edu>
> wrote:
>
> > OK by me to leave [ alone.  We could start with subsetByEntrez,
> > subsetByKEGG, subsetBySymbol, subsetByGOTERM, subsetByGOID.
> >
> > Utilities to generate GRanges for queries in each of these vocabularies
> > should, perhaps, be in the OrganismDb space?  Once those are in place
> > no additional infrastructure is necessary?
> >
> > On Sat, Sep 20, 2014 at 12:49 PM, Tim Triche, Jr. <tim.triche at gmail.com>
> > wrote:
> >
> > > Agreed with Sean, having tried implementing to "magical" alternative
> > >
> > > --t
> > >
> > > > On Sep 20, 2014, at 9:31 AM, Sean Davis <sdavis2 at mail.nih.gov>
> wrote:
> > > >
> > > > Hi, Vince.
> > > >
> > > > I'm coming a little late to the party, but I agree with Kasper's
> > > sentiment
> > > > that the less "magical" approach of using subsetByXXX might be the
> > > cleaner
> > > > way to go for the time being.
> > > >
> > > > Sean
> > > >
> > > >
> > > > On Sat, Sep 20, 2014 at 10:42 AM, Vincent Carey <
> > > stvjc at channing.harvard.edu>
> > > > wrote:
> > > >
> > > >>
> > > >>
> > >
> >
> https://github.com/vjcitn/biocMultiAssay/blob/master/vignettes/SEresolver.Rnw
> > > >>
> > > >> shows some modifications to [ that allow subsetting of SE by
> > > >> gene or pathway name
> > > >>
> > > >> it may be premature to work at the [ level.  Kasper suggested
> defining
> > > >> a suite of subsetBy operations that would accomplish this
> > > >>
> > > >> i think we could get something along these lines into the release
> > > without
> > > >> too much more work.  votes?
> > > >>
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> > > >>
> > > >> _______________________________________________
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> > > >
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> >
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> >
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> >
>
>
>
> --
> Computational Biologist
> Genentech Research
>
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>
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