Retrieve a allele frequency and LD scores for pre-defined lists of variants

Data frame includes 1000 genomes metadata including sample sizes, allele frequency and LD score, separated by 5 super populations (EUR = European, AFR = African, EAS = East Asian, AMR = Admixed American, SAS = South Asian)

Usage

afl2_list(variantlist = "reduced", opengwas_jwt = get_opengwas_jwt())

Arguments

variantlist

Choose pre-defined list. "reduced" = ~20k SNPs that are common in all super populations (default). "hapmap3" = ~1.3 million hm3 SNPs

opengwas_jwt

Used to authenticate protected endpoints. Login to https://api.opengwas.io to obtain a jwt. Provide the jwt string here, or store in .Renviron under the keyname OPENGWAS_JWT.

Value

Data frame containing ancestry specific LD scores and allele frequencies for each variant