Specify hg19 in using biomaRt getBM function
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lei.shang • 0
@60d92976
Last seen 29 days ago
Puerto Rico

Hi there, I was trying to use getBM to convert rsID to chromosome coordinate. My code is as below, but it give me h38 coordinates. Is there anyway to specify the genome build to get hg19 chromosome position?


snp_ids=scan(infile, character(), quote="")
snp_mart = useMart("ENSEMBL_MART_SNP", dataset="hsapiens_snp")
snp_attributes = c("refsnp_id", "chr_name", "chrom_start")

snp_locations = getBM(attributes=snp_attributes,
                      filters="snp_filter", 
                      values=snp_ids,
                      mart=snp_mart,
                      useCache=FALSE)
biomaRt biom • 93 views
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@james-w-macdonald-5106
Last seen 8 days ago
United States

You can use the archive.

> mart <- useEnsembl("ENSEMBL_MART_SNP","hsapiens_snp", "https://feb2014.archive.ensembl.org")
> getBM(c("refsnp_id","chr_name","chrom_start"), "snp_filter", "rs232423", mart)
  refsnp_id chr_name chrom_start
1  rs232423       21    22755223
> newmart <- useEnsembl("ENSEMBL_MART_SNP","hsapiens_snp")
> getBM(c("refsnp_id","chr_name","chrom_start"), "snp_filter", "rs232423", newmart)
  refsnp_id chr_name chrom_start
1  rs232423       21    21382903

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