infer_ancestry: Infer ancestry of GWAS dataset by matching against 1000...

In ieugwasr: Interface to the 'OpenGWAS' Database API

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

Description

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.

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

ieugwasr documentation built on July 2, 2024, 1:06 a.m.