run ld clump locally — run_clump • drugTargetScreen

run ld clump locally

Usage

run_clump(
  dat,
  ldRef,
  clump_kb = 1000,
  clump_r2 = 0.001,
  clump_p1 = 5e-08,
  clump_p2 = 1,
  threads = 36
)

Arguments

dat: data frame from TwoSampleMR::format_data() for exposure GWAS
ldRef: 1KG reference panel in plink format
clump_kb: clumping window. By default, clump_kb=1000
clump_r2: clumping r2 cutoff. By default, clump_r2=0.001
clump_p1: p-value threshold for the index SNP. By default, clump_p1=1
clump_p2: p-value threshold for the secondary SNP. By default, clump_p2=1
threads: number of threads used for plink