Hello,
I am using the R package "biomaRt" to find Ensembl IDs from a list of HGCN
gene IDs:
source("http://bioconductor.org/biocLite.R";)
biocLite("biomaRt",lib="~/src/Rlibs/")
library(biomaRt)
mart.ens <- useMart("ensembl", dataset = "hsapiens_gene_ensembl")
getBM(attributes=c("ensembl_gene_id", "hgnc_symbol"), filters="hgnc_symbol",
values="IPO8", mart=mart.ens)
ensembl_gene_id hgnc_symbol
1 ENSG00000133704 IPO8
It's working pretty well until a HGCN ID contains an apostrophe (here
"2'-PDE" is an alias for the gene "PDE12", see
here<http://www.genenames.org/data/hgnc_data.php?hgnc_id=25386>
):
getBM(attributes=c("ensembl_gene_id", "hgnc_symbol"), filters="hgnc_symbol",
values="2'-PDE", mart=mart.ens)
Error in getBM(attributes = c("ensembl_gene_id", "hgnc_symbol"), filters =
"hgnc_symbol", :
Query ERROR: caught BioMart::Exception: non-BioMart die():
not well-formed (invalid token) at line 1, column 322, byte 322 at
/usr/lib/perl5/XML/Parser.pm line 187
I know how to work around this for my own case, but would it be possible to
fix this for a future release?
Best regards,
Tim
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