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QTL lookup with LD-based proxy selection

Source: R/qtl_lookup.R
qtl_lookup.Rd

This function performs QTL lookup by integrating MR results with GWAS summary statistics and identifying proxy SNPs based on linkage disequilibrium (LD).

Usage

qtl_lookup(
  d,
  dat,
  panel = c("1000Genomes", "local"),
  p_threshold = 0.001,
  r2_threshold = 0.8,
  pop = "EUR",
  plink_bin = NULL,
  max_snps = 500,
  xlsx = NULL,
  verbose = TRUE
)

Arguments

d

Directory containing GWAS files.

dat

Data frame of MR results. Must contain: protein, id, pqtl, qtl, p_qtl, file_gwas.

panel

LD reference type: "1000Genomes" or "local".

p_threshold

P-value cutoff for selecting candidate SNPs.

r2_threshold

LD r^2 threshold for locus classification.

pop

1000 Genomes population (default "EUR").

Path to PLINK executable (required for local mode).

max_snps

Maximum SNPs used in LD computation.

xlsx

Optional Excel output path.

verbose

Logical; show progress messages.

Value

Updated dat with columns: proxy, p_proxy, rsq, classification.

Details

It supports:

  • 1000 Genomes LD reference (ieugwasr API)

  • Local PLINK reference panels (recommended for large-scale runs)

Loci are classified as:

  • same_locus (r^2 >= threshold)

  • independent_locus (r^2 < threshold)