afl2_list: Retrieve a allele frequency and LD scores for pre-defined...

In ieugwasr: Interface to the 'OpenGWAS' Database API

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

Description

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

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