Find instruments for use in MR from the MR Base 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 = TRUE,
  p2 = 5e-08,
  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: Logical; whether to clump results. The default is TRUE.
p2: Secondary clumping threshold. The default is 5e-8.
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: Force the analysis to extract results from the server rather than the MRInstruments package.

Value

data frame