[BioC] biomaRt with multiple databases/datasets?

T Joshi tejalonline at gmail.com
Thu Dec 4 14:37:58 CET 2008


Hi,
I was wondering if it is possible to use biomaRt package with multiple
databases and hence datasets. I want to retrieve GO information using
ensembl geneIDs. I use the following :

attributes=c("ensembl_gene_id","go_biological_process_id","go_cellular_component_id",
"go_biological_process_id", "go_biological_process_linkage_type",
"go_cellular_component_linkage_type","go_molecular_function_linkage_type"),

 and filters="ensembl_gene_id", for a "mart" object which uses ensembl
database.

I would like to see the names of pathways and reactions in which this
gene is involved. Could we do so using biomaRt?

cheers,
Josh



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