[BioC] problems with GenomeGraphs

[steffen at stat.Berkeley.EDU]

Hi Raphael,

I week ago there was an new release of Ensembl and a few of attributes in
Ensembl changed names.  These changes have been fixed in the GenomeGraphs
package available here:

http://bioconductor.org/packages/2.3/bioc/html/GenomeGraphs.html

Cheers,
Steffen

> Hi Jim and Steffen,
>
> I have been trying to use your package GenomeGraphs, but I get the
> following error when I tried the following code in the vignette:
>  > mart = useMart("ensembl", dataset = "hsapiens_gene_ensembl")
> Checking attributes and filters ... ok
>  > 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
>  >
>
> For you information, I use R 2.7 (64bit) on a OS X Leopard. Could you
> please let me know what I am doing wrong?
>
> Thanks!
>
> Raphael
>