[BioC] Where can I download/install old packages like 'org.Rn.eg.db' based on rn4?

[Hervé Pagès]

Hi ZQ,

On 01/01/2014 12:51 AM, Zhi-Qiang Ye wrote:
> Hi, thanks for your help.
>
> The information I need is the 'rn4' coordinates of Entrez Genes,  so I
> finally used the 'refGene' table and 'refLink' table downloaded from UCSC
> genome browser database under the directory of 'rn4', and got what I need.

Following Steve's original suggestion (but using the refGene table
instead of ensGene):

   library(GenomicFeatures)
   txdb <- makeTranscriptDbFromUCSC(genome='rn4', tablename='refGene')
   gn <- genes(txdb)

This gives you the 'rn4' coordinates of Entrez Genes:

   > head(gn)
   GRanges with 6 ranges and 1 metadata column:
               seqnames                 ranges strand |         gene_id
                  <Rle>              <IRanges>  <Rle> | <CharacterList>
     100034253     chrX [ 40301219,  40334396]      - |       100034253
     100036582     chr8 [ 18755584,  18756808]      + |       100036582
     100036765    chr12 [ 32898194,  32924599]      + |       100036765
     100049583     chr8 [114071508, 114072510]      - |       100049583
     100124593     chr8 [128569564, 128570618]      + |       100124593
     100125361    chr10 [ 45764849,  45775258]      - |       100125361
     ---
     seqlengths:
              chr1         chr2         chr3 ...        chrUn chrUn_random
         267910886    258207540    171063335 ...     75822765      6862066

   > head(as.character(mcols(gn)$gene_id))
   [1] "100034253" "100036582" "100036765" "100049583" "100124593" 
"100125361"

Note that makeTranscriptDbFromUCSC() downloads and uses the 'refGene'
and 'refLink' tables from UCSC for you in order to generate the
TranscriptDb object 'txdb'. In addition to being convenient, this
method also avoids some of the common pitfalls of downloading and
processing those tables "manually".

Cheers,
H.


> As for other information not related to the chromosomal locations, I just
> used the information in the package  'org.Rn.eg.db'.
>
> Maybe the maintainner can still provide official packages based on 'rn4',
> say, 'org.Rn4.eg.db', since annotation based on 'rn5' is not as complete as
> that based on 'rn4'.
>
> Best,
> ZQ
>
> On Sat, Dec 21, 2013 at 8:53 AM, Marc Carlson <mcarlson at fhcrc.org> wrote:
>
>> Steve is right.  You could go and do that.  However in this case we have
>> already done the work for you.  You can find a package here:
>>
>> http://www.bioconductor.org/packages/release/data/annotation/html/TxDb.
>> Rnorvegicus.UCSC.rn4.ensGene.html
>>
>> That should get you transcript locations for RN4.
>>
>> For more information about how you can make use of that resource and of
>> others like it, please be sure to also peak at our workflow:
>>
>> http://www.bioconductor.org/help/workflows/annotation/annotation/
>>
>>
>>    Marc
>>
>>
>>
>>
>>
>> On 12/18/2013 10:09 PM, Steve Lianoglou wrote:
>>
>>> Hi,
>>>
>>> On Wed, Dec 18, 2013 at 6:20 PM, Zhi-Qiang Ye <yezhiqiang at gmail.com>
>>> wrote:
>>>
>>>> Hi, all
>>>>
>>>>           I need to analysis genes whose chromosomal locations are based
>>>> on
>>>> the rat genome version rn4, so installed 'org.Rn.eg.db'. However, the
>>>> genome coordinate system is based on rn5.
>>>>
>>>>            Is there any way to get and install old versions of
>>>> 'org.Rn.eg.db'?
>>>>
>>> You might consider building a TranscriptDb object from rn4 annotations
>>> using the GenomicFeatures package:
>>>
>>> http://bioconductor.org/packages/release/bioc/html/GenomicFeatures.html
>>>
>>> Read through its vignette to figure out how to download and build a
>>> TranscriptDb from UCSC. It's going to be something like:
>>>
>>> R> library(GenomicFeatures)
>>> R> txdb <- makeTranscriptDbFromUCSC(genome='rn4', tablename='ensGene')
>>>
>>> Keep reading to figure out how to lookup genes/transcripts by
>>> (ensembl) transcript IDs, and I think you should be good to go.
>>>
>>> If you need to do sequence related analyses using these annotations,
>>> you can use the rn4 BSgenome object, to boot:
>>>
>>> http://bioconductor.org/packages/release/data/annotation/html/BSgenome.
>>> Rnorvegicus.UCSC.rn4.html
>>>
>>> HTH,
>>> -steve
>>>
>>>
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-- 
Hervé Pagès

Program in Computational Biology
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