[BioC] Using wildcard with BiomaRt:getBM

[steffen at stat.Berkeley.EDU]

Hi Daren,

Wildcards don't work.  I would query for all genes and then subselect in R.
This is not too heavy on the server as it is made for these type of batch
queries (you could store the result so you don't have to do it again for a
while):

ensembl = useMart("ensembl", dataset="hsapiens_gene_ensembl")
ids = getBM(attributes=c("hgnc_symbol","chromosome_name",
"start_position"), mart=ensembl)


should do it.

Cheers,
Steffen


>
> Hi,
>
> I need to obtain information via biomaRt for all members of interleukin.
> Trying the following command failed, apparently, getBM doesn't support
> regexp. I could download all the gene names and filter locally, but this
> will stress the hosting server and prolong communication time.
>
> getBM(attributes=c("hgnc_symbol, "start_position"), filter="hgnc_symbol",
> values="IL.*", mart=ensembl)
>
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