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

[Vincent Carey]

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, ]
>
>
yes, there has been some code around of that nature ... seems reasonable,
but perhaps a bit heavy.

there are identifier grouping translation facilities in GSEAbase that are
are also pertinent.

> ...
>
>
> 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?
>> > >>
>> > >>        [[alternative HTML version deleted]]
>> > >>
>> > >> _______________________________________________
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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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