[Bioc-devel] Replacing deprecated org.Hs.egCHR and friends
peter.langfelder at gmail.com
Tue Jan 13 20:02:56 CET 2015
On Tue, Jan 13, 2015 at 10:22 AM, Marc Carlson <mcarlson at fredhutch.org> wrote:
> Hi Peter,
> I would add that you can see a listing all the currently pre-manufactured
> TxDb packages here:
> 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:
> Hope this helps you to be better acquainted!
> 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
>> 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 (
>> 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.
>> 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.
>>> R Under development (unstable) (2014-11-24 r67057)
>>> Platform: x86_64-unknown-linux-gnu (64-bit)
>>>  LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
>>>  LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
>>>  LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
>>>  LC_PAPER=en_US.UTF-8 LC_NAME=C
>>>  LC_ADDRESS=C LC_TELEPHONE=C
>>>  LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
>>> attached base packages:
>>>  parallel stats4 stats graphics grDevices utils datasets
>>>  methods base
>>> other attached packages:
>>>  org.Hs.eg.db_3.0.0 RSQLite_1.0.0 DBI_0.3.1
>>>  AnnotationDbi_1.29.12 GenomeInfoDb_1.3.12 IRanges_2.1.35
>>>  S4Vectors_0.5.16 Biobase_2.27.1 BiocGenerics_0.13.4
>>>  BiocInstaller_1.17.3
>>> loaded via a namespace (and not attached):
>>>  tools_3.2.0
>>> Bioc-devel at r-project.org mailing list
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