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:
I am new to biomaRt. My question might therefore have a really obvious
When I tried running the following command in R, R crashed each time.
snp = useMart("snp", dataset="hsapiens_snp")
filters=c("ensembl_gene"), values="ENSG00000067225", mart=snp)
What am I doing wrong?
Thank you so much in advance for your help,
Department of Genetic Epidemiology
Georg-August University Göttingen
Office Phone: +49 551 39 14234