[R] Error using getBM() to query BioMart archives

[Martin Morgan]

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Martin

Aaron Wolen <wolenar at vcu.edu> writes:

> I'm trying to identify the positions of all genes within a specific
> chromosomal region using biomart. When using the current biomart
> database I'm able to do this without issue. However, I need to use
> build 36 of the mouse genome which was last included in ensembl mart
> 46. I selected this mart and the mouse dataset as follows:
>
> mart<-useMart(biomart="ensembl_mart_46", host="www.biomart.org",
> path="/biomart/martservice", port=80, archive=TRUE)
>
> mart<-useDataset("mmusculus_gene_ensembl", mart=mart)
>
> I'm able to list the available attributes and filters just fine, but
> when I attempt to actually retrieve data using getBM() I receive the
> following error:
>
>  > genes<-getBM(attributes=c("ensembl_gene_id", "external_gene_id",
> "description", "chromosome_name", "start_position",
> "transcript_start"),
> + filters=c("chromosome_name","start","end"),
> + values=list(12,40000000,70000000),
> + mart=mart)
> Error in listFilters(mart, what = "type") :
>    The function argument 'what' contains an invalid value: type
> Valid are: name, description, options, fullDescription
>
> The same error is returned if I check to see what value type is
> required for a particular filter:
>
>  > filterType("chromosome_name", mart=mart)
> Error in listFilters(mart, what = "type") :
>    The function argument 'what' contains an invalid value: type
> Valid are: name, description, options, fullDescription
>
> I'd really appreciate some help with this issue.
>
> Cheers,
> Aaron
>
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Martin Morgan
Computational Biology / Fred Hutchinson Cancer Research Center
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