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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