[Bioc-devel] Replacing deprecated org.Hs.egCHR and friends

[James W. MacDonald]

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.langfelder at 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 at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>



-- 
James W. MacDonald, M.S.
Biostatistician
University of Washington
Environmental and Occupational Health Sciences
4225 Roosevelt Way NE, # 100
Seattle WA 98105-6099

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