[Bioc-devel] GenomicFeatures makeTranscriptDbFromUCSC Table Missing

[Valerie Obenchain]

Hi Dario,

The makeTranscriptDbFromUCSC uses functions in rtracklayer to retrieve 
data from the Table Browser (http://genome.ucsc.edu/cgi-bin/hgTables) .
You'll see that the ensGtp table is no longer there for hg18.

Herve found that the ensGene table has a column that does contain the 
Ensembl gene id so the join with the ensGtp table is no longer needed.
He committed a fix that extracts the gene ids from this column. It look 
like there are still some other problems with GenomicFeatures
(still not passing check in release) but at least this one is fixed.

Valerie



On 10/07/2011 11:20 AM, Hervé Pagès wrote:
> Hi Dario,
>
> Sorry that I didn't see your email earlier. Thanks for the report.
> We also have this problem here:
>
>
> http://bioconductor.org/checkResults/2.8/bioc-LATEST/GenomicFeatures/lamb1-checksrc.html 
>
>
> I'm currently looking at this. Will come back soon.
>
> H.
>
>
> On 11-09-13 08:00 PM, Dario Strbenac wrote:
>> Hello,
>>
>> I noticed that getting an ENSEMBL gene table for the hg18 assembly 
>> doesn't work
>>
>>> hg18Ens<- makeTranscriptDbFromUCSC(genome="hg18",tablename="ensGene")
>> Download the ensGene table ... OK
>> Download the ensGtp table ... Error in normArgTable(value, x) : 
>> unknown table name 'ensGtp'
>>
>> but for hg19 it does.
>>
>> makeTranscriptDbFromUCSC(genome="hg19",tablename="ensGene")
>> Download the ensGene table ... OK
>> Download the ensGtp table ... OK
>> Extract the 'transcripts' data frame ... OK
>> Extract the 'splicings' data frame ... OK
>> Download and preprocess the 'chrominfo' data frame ... OK
>> Prepare the 'metadata' data frame ... OK
>> Make the TranscriptDb object ... OK
>>
>> I can download ensGtp hg18 manually from the UCSC website.
>>
>> --------------------------------------
>> Dario Strbenac
>> Research Assistant
>> Cancer Epigenetics
>> Garvan Institute of Medical Research
>> Darlinghurst NSW 2010
>> Australia
>>
>> _______________________________________________
>> Bioc-devel at r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>>
>
>