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Infer ancestry of GWAS dataset by matching against 1000 genomes allele frequencies

Source: R/afl2.r
infer_ancestry.Rd

Uses ~20k SNPs selected for common frequency across 5 major super populations

Usage

infer_ancestry(d, snpinfo = NULL, opengwas_jwt = get_opengwas_jwt(), ...)

Arguments

d

Data frame containing at least rsid and eaf columns. e.g. output from associations

snpinfo

Output from afl2_list, afl2_rsid or afl2_chrpos. If NULL then afl2_list() is used by default

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.

...

Additional arguments passed to afl2_list()

Value

data frame ordered by most likely ancestry, each row represents a super population and cor column represents the correlation between the GWAS dataset and the 1000 genomes super population allele frequencies