Question

Specify hg19 in using biomaRt getBM function

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lei.shang • 0

@60d92976

Last seen 2.5 years 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 • 2.5k views

ADD COMMENT • link updated 2.5 years ago by James W. MacDonald 65k • written 2.5 years ago by lei.shang • 0

score 2 · Accepted Answer · 2021-10-28

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