Thanks for the clarification. Isn't there a way via active bindings to preserve the interfaces conferred by e.g., illuminaHumanv1CHRLOC, so that queries to the object (no longer a Bimap) succeed with the endorsed metadata? the chipDb packages would be revised to use a new protocol for these queries that go through TxDb.
On Mon, Sep 22, 2014 at 8:38 PM, Marc Carlson <mcarl...@fhcrc.org> wrote: > Hi Vince, > > So if you wanted to do this manually, then the thing you would want to do > is to get a gene ID from the probe and to take that to a TranscriptDb > object (again: that is if you wanted to do it manually). Alternatively, if > you had an OrganismDb object then this association would be handled for you > (where it would be spelled out explicitly). The explicit nature is what we > are after here since where a gene is expected to be (chromosome wise) can > depend on the build of genome you are using. As people move between > standard genomes and eventually to custom ones, we needed to decouple this > kind of data from the organism packages (which are only ever intended to > hold gene-centered data). > > Marc > > > > On 09/21/2014 08:21 AM, Vincent Carey wrote: > >> On Sun, Sep 21, 2014 at 11:07 AM, Martin Morgan <mtmor...@fhcrc.org> >> wrote: >> >> On 09/21/2014 07:44 AM, Vincent Carey wrote: >>> >>> this is coming out of the build system for GGtools ... not easy to find >>>> as >>>> the >>>> >>>> problem seems to cause emission of megabytes of warnings >>>> >>>> >>>> illuminaHumanv1CHR is deprecated as the data is better accessed from >>>> >>>> another location. Please use an appropriate TxDb object or package >>>> for >>>> >>>> this kind of data. >>>> >>>> >>>> i don't see the deprecation in the doc for illuminaHumanv1.db and i >>>> cannot >>>> >>>> get a get() to throw it. i also don't see this on the devel version >>>> package landing page >>>> >>>> Marc will likely reply on Monday. But the intention is that the CHR >>> bimaps >>> in *db packages Marc curates are being deprecated. The deprecation itself >>> occurs in AnnotationDbi, I think. The reason is the lack of provenance >>> for >>> this information -- what genome build does it refer to? -- and its >>> availability from other sources (i.e., the TxDb packages) with >>> provenance. >>> >>> >>> Nice to hear about the streamlining and improved provenance. I confess >> I >> don't >> see how to get a probe-chr mapping out of TxDb -- is there something new >> in >> there? >> A select operation that can resolve queries about manufacturer >> identifiers? >> >> >> illuminaHumanv1CHR >>>> >>> illuminaHumanv1CHR is deprecated as the data is better accessed from >>> another location. Please use an appropriate TxDb object or package for >>> this kind of data. >>> CHR map for chip illuminaHumanv1 (object of class "ProbeAnnDbBimap") >>> >>> I think this is currently a message, but should be a warning. >>> >>> AnnotationDbi is not building successfully, so its biocLite() version and >>> landing page are not in sync with an svn checkout (used by the build >>> system); to replicate on your own system requires an svn install, at >>> least >>> until AnnotationDbi builds successfully. >>> >>> OK, so I can get the message now. But I think more details need to be >> supplied if >> we are to drop references to *CHR. >> >> >> I guess the megabytes of warnings come from code in GGtools or elsewhere; >>> maybe there's a >>> >> >> Indeed. Perhaps unrelated to this. >> >> convenient way of aggregating them (hopefully before throwing the warning, >> >>> since that can be quite expensive). >>> >>> Martin >>> >>> >>> [[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 >> > > [[alternative HTML version deleted]] _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel