ld_reflookup {ieugwasr}

Check which rsids are present in a remote LD reference panel

Description

Provide a list of rsids that you may want to perform LD operations on to check if they are present in the LD reference panel. If they are not then some functions e.g. ld_clump will exclude them from the analysis, so you may want to consider how to handle those variants in your data.

Usage

ld_reflookup(rsid, pop = "EUR", opengwas_jwt = get_opengwas_jwt())

Arguments

rsid

Array of rsids to check

pop

Super-population to use as reference panel. Default = "EUR". Options are "EUR", "SAS", "EAS", "AFR", "AMR"

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.#' @param bfile If this is provided then will use the API. Default = NULL

Value

Array of rsids that are present in the LD reference panel