[Bioc-devel] GenomicFeatures makeTranscriptDbFromUCSC Table Missing

[Dario Strbenac]

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