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