[BioC] getting Locus Link ids from gene symbol

[Steffen Durinck]

Hi Alex,

You could use the biomaRt package for this, here the code to do it:

 >library(biomaRt)
 >ensembl=useMart("ensembl",dataset="hsapiens_gene_ensembl")
 >map = getBM(c("hgnc_symbol","entrezgene"), 
filters=c("hgnc_symbol","with_entrezgene"), 
values=list(c("Btk","Casp8"),TRUE), mart=ensembl)

it should give:

 >unique(map)

  hgnc_symbol entrezgene
1       CASP8        841
6         BTK        695



Cheers,
Steffen


Alex Tsoi wrote:
> Dear all,
>
> I have a list of gene symbols (eg. Btk, Casp8), and I would like to get
> their corresponding gene locus link IDs.
>
> Could anyone show me the ways I could do it.
>
> Greatly appreciate for any suggestion.
>
> Thanks,
> Alex-
>
> 	[[alternative HTML version deleted]]
>
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-- 
Steffen Durinck, Ph.D.

Oncogenomics Section
Pediatric Oncology Branch
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