[BioC] attributes in GenomeGraphs

Amanda Miotto a.miotto at griffith.edu.au
Tue Aug 5 05:04:35 CEST 2008

In regards to the library GenomeGraphs, when I try to define a Gene, I get
the following error. I am following the instructions from The GenomeGraphs
user’s guide by Steffen Durinck∗and James Bullard†. Where would I be going
wrong? Also, I am curious about the structure of gene, as I am trying to
replicate it with RMySQL, having set up a mysql identical to the ensembl
one. In the list listAttributes, ensembl_gene_id is in there.

> gene = new("Gene", id = "ENSG00000095203",type = "ensembl_gene_id",
biomart = mart)
Error in getBM(c("structure_gene_stable_id",
"structure_transcript_stable_id",  :
  Invalid attribute(s): structure_exon_stable_id,
structure_exon_chrom_start, structure_exon_chrom_end, structure_exon_rank
Please use the function 'listAttributes' to get valid attribute names

Amanda Miotto
a.miotto at griffith.edu.au

Software Engineer.
Research Computing Services
Griffith University, NATHAN 4111, AUSTRALIA
Phone:  +61 7 37354419  Fax:  +61 7 37356650
Web:    http://eResearch.griffith.edu.au/

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