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

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.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