Thanks all! On Tue, Jan 13, 2015 at 10:22 AM, Marc Carlson <mcarl...@fredhutch.org> wrote: > Hi Peter, > > I would add that you can see a listing all the currently pre-manufactured > TxDb packages here: > > http://www.bioconductor.org/packages/devel/BiocViews.html#___TxDb > > And for convenience you can also use an OrgansimDb package to connect the > contents of the TxDb package with the older org packages. You can learn > more about those (and the other annotation resources) here: > > http://www.bioconductor.org/help/workflows/annotation/annotation/ > > Hope this helps you to be better acquainted! > > > Marc > > > > > On 01/13/2015 07:30 AM, James W. MacDonald wrote: >> >> Hi Peter, >> >> This isn't a devel question. Next time please ask this sort of thing on >> the >> support site. >> >> As for the message, it seems pretty clear to me. The org.Hs.eg.db package >> doesn't have the chromosomal location data any more, but the relevant TxDb >> package does have those data, in a much more useful format. The message >> can't be any more explicit than that, as there is more than one TxDb >> package for human. >> >> You could have hypothetically gone to the annotation data page ( >> http://bioconductor.org/packages/release/BiocViews.html#___AnnotationData) >> and searched for, say 'TxDb', in which case you would see three packages >> with names like TxDb.Hsapiens.UCSC.hg19.knownGene. Which one you decide to >> use is dependent on the build/source you care about. >> >> And if you are completely unfamiliar with these packages, you need to read >> the GenomicFeatures vignette. >> >> Best, >> >> Jim >> >> >> >> On Tue, Jan 13, 2015 at 12:34 AM, Peter Langfelder < >> peter.langfel...@gmail.com> wrote: >> >>> Hi all, >>> >>> can anyone please explain or point me to an explanation of how to >>> replace org.Hs.egCHR and friends that appear to be deprecated in the >>> devel version? The deprecation message isn't very helpful. Thanks! >>> >>> x = org.Hs.egCHR >>> Warning message: >>> In (function () : >>> org.Hs.egCHR is deprecated. Please use an appropriate TxDb object or >>> package for this kind of data. >>> >>> sessionInfo() >>> >>> R Under development (unstable) (2014-11-24 r67057) >>> Platform: x86_64-unknown-linux-gnu (64-bit) >>> >>> locale: >>> [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C >>> [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 >>> [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 >>> [7] LC_PAPER=en_US.UTF-8 LC_NAME=C >>> [9] LC_ADDRESS=C LC_TELEPHONE=C >>> [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C >>> >>> attached base packages: >>> [1] parallel stats4 stats graphics grDevices utils datasets >>> [8] methods base >>> >>> other attached packages: >>> [1] org.Hs.eg.db_3.0.0 RSQLite_1.0.0 DBI_0.3.1 >>> [4] AnnotationDbi_1.29.12 GenomeInfoDb_1.3.12 IRanges_2.1.35 >>> [7] S4Vectors_0.5.16 Biobase_2.27.1 BiocGenerics_0.13.4 >>> [10] BiocInstaller_1.17.3 >>> >>> loaded via a namespace (and not attached): >>> [1] tools_3.2.0 >>> >>> _______________________________________________ >>> Bioc-devel@r-project.org mailing list >>> https://stat.ethz.ch/mailman/listinfo/bioc-devel >>> >> >> > > _______________________________________________ > Bioc-devel@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/bioc-devel
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