Hi,
On 01/13/2015 10:22 AM, Marc Carlson 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/
Maybe the warning could display this link or whatever pointer to
the place where mapping Entrez Gene ids to chromosome is explained.
Note that extracting this mapping from a TxDb package is a 3-liner:
library(TxDb.Hsapiens.UCSC.hg19.knownGene)
txdb <- TxDb.Hsapiens.UCSC.hg19.knownGene
select(txdb, keys=keys(txdb), columns=c("GENEID", "TXCHROM"),
keytype="GENEID")
so maybe the warning message could just display that...
Cheers,
H.
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
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Hervé Pagès
Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
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