Chromosomal Position to rsID and Allele Frequency
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Entering edit mode
19 months ago
gtasource ▴ 60

Im using the biomart bioconductor package to find allele frequencies/rsIDs based upon chromosomal location. Here's my code:

 mart <- useEnsembl(biomart = 'ENSEMBL_MART_SNP', 
           dataset = 'hsapiens_snp',
           version = "GRCh37")

  mutations <- getBM(attributes = c('refsnp_id', 'allele', 'chrom_start'), 
        filters = c('chr_name','start','end'), 
        values = list(chrom, start, end), 
        mart = mart)  

Issue I'm having is:

1.) I'm getting multiple hits per chromosomal position, and I just don't know how to narrow this down (since Im dealing with hundreds of SNPs.)

2.) For SNPs that don't have rsIDs, is there anyway to try to find allele frequencies? Manually searching some of these variants aren't coming up with anything

Cheers

frequency allele snps biomart • 460 views
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