On Sat, Oct 11, 2014 at 5:17 PM, Michael Lawrence <lawrence.mich...@gene.com > wrote:
> But what it would do exactly? > > Probably would want to be able to extract a gene list from a TxDb, then > extract the desired type of structure from the TxDb. > > Not too bad right now, but it would be nice to leverage the identifier > type information on the gene list object. > > Currently: > tx <- transcripts(txdb, vals=list(gene_id=genes)) > > Proposed: > tx <- transcripts(txdb[GeneList]) > yes, that makes sense. i don't go to txdb's as naturally as i should. > > > > On Sat, Oct 11, 2014 at 10:49 AM, Martin Morgan <mtmor...@fhcrc.org> > wrote: > >> On 10/11/2014 08:41 AM, Vincent Carey wrote: >> >>> Is there anything on the order of as([GeneSet], "GRanges") around? >>> >> >> no, I don't think so; obviously of use and following a common theme. >> Martin >> >> >> >>> 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 >>> >>> >> >> -- >> Computational Biology / Fred Hutchinson Cancer Research Center >> 1100 Fairview Ave. N. >> PO Box 19024 Seattle, WA 98109 >> >> Location: Arnold Building M1 B861 >> Phone: (206) 667-2793 >> > > [[alternative HTML version deleted]] _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel