Find instruments for use in MR from the OpenGWAS database — extract

This function searches for GWAS significant SNPs (for a given p-value) for a specified set of outcomes. It then performs LD based clumping to return only independent significant associations.

Usage

extract_instruments(
  outcomes,
  p1 = 5e-08,
  clump = 1,
  r2 = 0.001,
  kb = 10000,
  opengwas_jwt = ieugwasr::get_opengwas_jwt(),
  force_server = FALSE
)

Arguments

outcomes: Array of outcome IDs (see available_outcomes()).
p1: Significance threshold. The default is 5e-8.
clump: Whether to clump results (1) or not (0). Default is 1. (TRUE and FALSE are also allowed for backwards compatibility.)
r2: Clumping r2 cut off. The default is 0.001.
kb: Clumping distance cutoff. The default is 10000.
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.
force_server: Whether to search through pre-clumped dataset or to re-extract and clump directly from the server. The default is FALSE.

Value

data frame