Hi,

I am using bioMart to convert rsIDs to chromosome and positions. I also need to keep the rsIDs in the final dataset but I cannot find this option in the attributes.

I am showing my code here and specifically the one with the attributes. Could you please advise?

library(biomaRt);

human <- useMart(host="www.ensembl.org", "ENSEMBL_MART_ENSEMBL", dataset="hsapiens_gene_ensembl");

listMarts(host="www.ensembl.org");

attributes = listAttributes(human);

attributes[1:30,];

snp_ids = data$rsidonly;

snp_attributes = c("ensembl_gene_id", "chromosome_name", "start_position", "end_position", "transcript_start", "transcript_end");

snp_locations = getBM(attributes=snp_attributes, filters="chromosomal_region", values=snp_ids, mart=human);

Thank you,

Elena

I'm not sure you can query the genes database with rsIDs, but you should be able to get the information from the variation database.

library(biomaRt)
human_variation = useMart(biomart = "ENSEMBL_MART_SNP", dataset = "hsapiens_snp") 

snp_ids = "rs746229459"

snp_attributes = c("refsnp_id", 
                   "ensembl_gene_stable_id", 
                   "chr_name", 
                   "chrom_start", 
                   "chrom_end", 
                   "ensembl_transcript_stable_id");

snp_locations = getBM(attributes = snp_attributes, 
                      filters = "snp_filter", 
                      values = snp_ids, 
                      mart = human_variation);

snp_locations
    refsnp_id ensembl_gene_stable_id         chr_name chrom_start chrom_end
1 rs746229459        ENSG00000201015                6    67541718  67541718
2 rs746229459        ENSG00000252303 CHR_HG2128_PATCH    67541718  67541718
  ensembl_transcript_stable_id
1              ENST00000364145
2              ENST00000516494