[BioC] biomaRt * search

Paul Hammer paul.hammer at p-t-p.de
Thu Nov 5 18:10:21 CET 2009


Dear folks,

I try to search for all PDE genes within the biomaRt Ensembl database. I 
am looking for a simple code for searching with the * symbol like under 
linux (e.g. grep function). here my imaginary, not working code:

library(biomaRt)
ensembl = useMart("ensembl", dataset = "hsapiens_gene_ensembl")
PDE_infos = getBM(attributes = c("hgnc_symbol", "ensembl_gene_id"), 
filters = "hgnc_symbol", values = "*PDE*", mart = ensembl)

Is there any easy way to do such a * search? I mean I could first 
download all genes and then I could filter via regular expression for 
PDE genes. But I guess there is a way to use * in R or?

Thanks,
Paul



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