Hi Saskia,
I tried this query in R and it indeed seems not to return any result.
Using the BioMart web interface at www.biomart.org, this query take a
very long time to return a result and that might be why you have to
wait a long time in R to get something back as well. We have to ask
the BioMart developers why this is using the following XML query.
<?xml version='1.0' encoding='UTF-8'?><!DOCTYPE Query><Query
virtualSchemaName = 'default' uniqueRows = '1' count = '0'
datasetConfigVersion = '0.6' requestid= "biomaRt"> <Dataset name =
'hsapiens_snp'><Attribute name = 'refsnp_id'/><Attribute name =
'ensembl_gene_stable_id'/><Filter name = 'ensembl_gene' value =
'ENSG00000067225' /></Dataset></Query>
If you query the previous version of Ensembl (v61), the query returns
a result very quickly, so that might be a solution for you until the
problem with the current mart is resolved:
> snp=useMart(
> 'ENSEMBL_MART_SNP',dataset='hsapiens_snp',host="feb2011.archive.ensembl.org")
> ensemblref<-getBM(attributes= c("refsnp_id","ensembl_gene_stable_id"),
filters=c("ensembl_gene"), values="ENSG00000067225", mart=snp)
> head(ensemblref)
refsnp_id ensembl_gene_stable_id
1 rs10514 ENSG00000067225
2 rs762804 ENSG00000067225
3 rs890312 ENSG00000067225
4 rs916133 ENSG00000067225
5 rs1037680 ENSG00000067225
6 rs1062430 ENSG00000067225
Cheers,
Steffen
Hello,
I am new to biomaRt. My question might therefore have a really obvious
solution.
When I tried running the following command in R, R crashed each time.
library(biomaRt)
snp = useMart("snp", dataset="hsapiens_snp")
ensemblref<-getBM(attributes= c("refsnp_id","ensembl_gene_stable_id"),
filters=c("ensembl_gene"), values="ENSG00000067225", mart=snp)
What am I doing wrong?
Thank you so much in advance for your help,
Saskia Freytag
--
Saskia Freytag
Department of Genetic Epidemiology
Georg-August University Göttingen
Humboltallee 32
37073 Göttingen
Germany
Office Phone: +49 551 39 14234
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