SNP names Biomart error: Invalid filters(s): snp_filter

Question

[PeterKW]

Hi everyone,

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.

[zx8754]

Error is clear, "snp_filter" is not a valid filter name, check the output of listFilters(ensembl).

[PeterKW]

Thanks for the feedback. I have gone through the listFilters(ensembl) and listAttributes(ensembl) and I am not sure what I should set for both to get the stable snp IDs for the rs numbers.

Please help.

Answer 1

[Kevin Blighe]

Hi,

You are using the incorrect dataset, which is why that filter cannot be found; In addition, ensembl_gene_id is not an attribute in the SNP biomaRt.

Here is a reproducible solution:

require(biomaRt)

ensembl <- useMart('ENSEMBL_MART_SNP', dataset = 'btaurus_snp')

getBM(
  attributes = c('refsnp_id',
    'chr_name', 'chrom_start','chrom_end',
    'allele', 'mapweight', 'validated', 'allele_1', 'minor_allele',
    'minor_allele_freq', 'minor_allele_count',
    'synonym_name', 'ensembl_gene_stable_id'),
  filters = c('snp_filter'),
  values = 'rs17870417',
  mart = ensembl,
  uniqueRows = TRUE)


   refsnp_id chr_name chrom_start chrom_end allele mapweight
1 rs17870417        1    78737731  78737731    A/G         1
                        validated allele_1 minor_allele minor_allele_freq
1 Frequency,Multiple_observations       NA           NA                NA
  minor_allele_count synonym_name ensembl_gene_stable_id
1                 NA           NA     ENSBTAG00000044001

Example for Homo sapeins SNP biomaRt here: How to retrieve Gene name from SNP ID using biomaRt

Kevin