I have seen a similar question (here) but I can't figure out how the issue was solved.
I have a list (> 500k) of SNPs rs numbers and would like to get their corresponding stable snp names. The code that I am running to test for one snp before I have a go with the whole list is:
library(biomaRt) ensembl = useDataset("btaurus_gene_ensembl", mart = ensembl) getBM(attributes=c("ensembl_gene_id","variation_name"),filters = c("snp_filter"), values="rs17870417", mart=ensembl, uniqueRows=TRUE)
But I get this error:
Error in getBM(attributes = c("ensembl_gene_id", "variation_name"), filters = c("snp_filter"), : Invalid filters(s): snp_filter Please use the function 'listFilters' to get valid filter names
How can I solve this error or is there another filter option for "snp_filter"? I can find the snp name on the ensembl website. Thanks in advance.