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

5 messages · James W. MacDonald, Marc Carlson, Peter Langfelder +1 more

Original
Peter Langfelder
# 
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
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:

            

      
      
      
    

        

      
      
    

        

  
    

      
      
    

  


  


      

    

    

      
      

        


  

        

      Marc Carlson
    

    

      
      #
    

  


  

      
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:

            

      
      
      
    

        

      
      
    

            

      
      
      
    

  
  


  


      

    

    

      
      

        


  

        

      Peter Langfelder
    

    

      
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Thanks all!

        
On Tue, Jan 13, 2015 at 10:22 AM, Marc Carlson <mcarlson at fredhutch.org> wrote:

            

      
      
      
    

        

      
      
    

            

      
      
      
    

        

      
      
    

  
  


  


      

    

    

      
      

        


  

        

      Hervé Pagès
    

    

      
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Hi,

        
On 01/13/2015 10:22 AM, Marc Carlson wrote:

            

      
      
      
    

        
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.