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

[Hervé Pagès]

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

-- 
Hervé Pagès

Program in Computational Biology
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