[Bioc-devel] GenomicFeatures makeTranscriptDbFromUCSC Table Missing
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
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