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

Source: R/afl2.r
afl2_list.Rd

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 = c("reduced", "hapmap3")[1],
  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