GLOW Omnibus Test from Pre-Computed P-values

Performs the GLOW omnibus test when individual variant p-values are already computed. Reconstructs Z-scores from p-values and their signs, then runs the omnibus test pipeline via run_bsf_tests().

GLOW_Omni_byP(
  Pvalues,
  Zsigns,
  M,
  Bstar,
  PI,
  test_specs = NULL,
  include_snv_cct = TRUE,
  return_weights = FALSE,
  ...
)

Arguments

Pvalues

Numeric vector of variant-level p-values (length m, in \([0,1]\)).

Zsigns

Numeric vector of effect direction signs (length m, +1 or -1).

M

Correlation matrix of Z-scores (m x m).

Bstar

Numeric vector of scaled effect sizes (length m).

PI

Numeric vector of variant-importance scores (length m, in \([0,1]\)).

test_specs

List of test spec lists (default: NULL uses default_test_specs).

include_snv_cct

Logical (default TRUE). Append SNV-level and final omnibus CCT rows.

return_weights

Logical (default FALSE). If TRUE, attach the internally-assembled weight matrix to the result (forwarded from run_bsf_tests).

...

Additional arguments passed to run_bsf_tests.

Value

Same structure as GLOW_Omni.

Details

Algorithm:

1. Reconstruct Z-scores: \(Z = \Phi^{-1}(1 - p/2) \times sign\)

2. Call run_bsf_tests() with reconstructed Z-scores

CRITICAL: The correlation matrix M must reflect the Z-score correlation structure, not the adjusted p-value structure.

See also

GLOW_Omni for omnibus test with Z-scores getZ_marg_score_binary_SPA for SPA-adjusted p-values