Retrieve SNP pairwise LD from locuscompare database

Source: R/download.R

SNP pairwise lD are calculated based on 1000 Genomes Project Phase 3 version 5. For storage-efficiency, the output will only include SNPs with r2 > 0.2 with the input SNP.

retrieveLD(chr, snp, population)

Arguments

chr

(string) Chromosome name. e.g. '22'. Notice that the name should not contain 'chr'.

snp

(string) SNP rsID.

population

(string) One of the 5 popuations from 1000 Genomes: 'AFR', 'AMR', 'EAS', 'EUR', and 'SAS'.

Value

A data.frame object.

Examples

ld <- retrieveLD('6', 'rs9349379', 'AFR')