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Extract Independent Variants (Updated to use configuration)

extract_independent_variants.Rd

Extracts independent variants from GWAS summary statistics using clumping with support for re-randomization and configuration.

Usage

extract_independent_variants(
  exposure_data,
  p_threshold = 5e-05,
  etamean = 0.5,
  ref_panel = NULL,
  clump_r2 = 0.001,
  clump_kb = 10000,
  temp_dir = NULL,
  verbose = TRUE,
  rerand = TRUE,
  plink_path = NULL
)

Arguments

exposure_data

Exposure GWAS summary statistics

p_threshold

P-value threshold for selecting significant SNPs

etamean

Mean of the random variable for re-randomization

ref_panel

Path to reference panel for LD clumping

clump_r2

Clumping r-squared threshold

clump_kb

Clumping window size in kb

temp_dir

Directory for temporary files

verbose

Whether to print detailed progress messages

rerand

Whether to use re-randomization for SNP selection

Path to plink executable

Value

A vector of independent SNP IDs