Entering edit mode
8 weeks ago
a.wagen • 0
I am trying to annotate a list of snps with the ENSG gene number using biomaRt. I need to use ensemble version 91. I have built the following query:
snps = c("rs201327123" "rs141149254" "rs114420996" "rs62637817") ensembl.snp = useEnsembl(biomart="snps", version=91) mart.snp <- useMart(biomart = "ENSEMBL_MART_SNP") dataset.snp <- useDataset(dataset = "hsapiens_snp", mart=mart.snp) getBM(attributes=c('refsnp_id', 'ensembl_gene_stable_id'), filters = 'snp_filter', values = snps, mart = dataset.snp)
However the output does not include any gene ids (all are listed as NA's).
Any thoughts very much appreciated!
Thanks - that worked.