Is there anything on the order of as([GeneSet], "GRanges") around?
On Sat, Sep 20, 2014 at 11:34 PM, Gabe Becker <becker.g...@gene.com> wrote: > Sean and Vincent, > > The goal of what we are doing builds off of what Martin has in GSEABase. > We were looking to see how much benefit we can get with something > lighter-weight that lies between indistinguishable character vectors and > the full machinery of GeneSets. > > Either way, it seems like formalizing the semantic information is a way to > do what you want. Furthermore, these classed id objects can be created > automatically when there is contextual information e.g. during queries to > databases (or db-like objects), and then simply added to metadata > DataFrames and re-used. > > ~G > > > > > On Sat, Sep 20, 2014 at 12:19 PM, Sean Davis <sdav...@mail.nih.gov> wrote: > >> >> >> On Sat, Sep 20, 2014 at 3:11 PM, Gabe Becker <becker.g...@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 < >>> st...@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.tri...@gmail.com> >>> > wrote: >>> > >>> > > Agreed with Sean, having tried implementing to "magical" alternative >>> > > >>> > > --t >>> > > >>> > > > On Sep 20, 2014, at 9:31 AM, Sean Davis <sdav...@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 < >>> > > st...@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]] >>> > > >> >>> > > >> _______________________________________________ >>> > > >> Bioc-devel@r-project.org mailing list >>> > > >> https://stat.ethz.ch/mailman/listinfo/bioc-devel >>> > > > >>> > > > [[alternative HTML version deleted]] >>> > > > >>> > > > _______________________________________________ >>> > > > Bioc-devel@r-project.org mailing list >>> > > > https://stat.ethz.ch/mailman/listinfo/bioc-devel >>> > > >>> > >>> > [[alternative HTML version deleted]] >>> > >>> > _______________________________________________ >>> > Bioc-devel@r-project.org mailing list >>> > https://stat.ethz.ch/mailman/listinfo/bioc-devel >>> > >>> >>> >>> >>> -- >>> Computational Biologist >>> Genentech Research >>> >>> [[alternative HTML version deleted]] >>> >>> _______________________________________________ >>> Bioc-devel@r-project.org mailing list >>> https://stat.ethz.ch/mailman/listinfo/bioc-devel >>> >> >> > > > -- > Computational Biologist > Genentech Research > [[alternative HTML version deleted]] _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel