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

[Vincent Carey]

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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