Post-process Fine-mapping Fits — postprocess_finemapping

Applies method-aware post-processing to one or more SuSiE-family fits and builds both a method-specific result list and shared top-loci tables.

Usage

postprocess_finemapping_fits(
  fits,
  data_x,
  data_y = NULL,
  X_scalar = 1,
  y_scalar = 1,
  maf = NULL,
  coverage = NULL,
  secondary_coverage = c(0.7, 0.5),
  signal_cutoff = 0.1,
  other_quantities = NULL,
  prior_eff_tol = 1e-09,
  min_abs_corr = 0.8
)

Arguments

fits: Named list of fine-mapping fits. Names define method identity, for example susie, susie_inf, susie_rss, mvsusie, or fsusie.
data_x: Genotype matrix, LD/correlation matrix, or other method-specific input used for credible-set purity and correlations.
data_y: Phenotype vector/matrix or summary statistics. Default NULL.
X_scalar: Scaling factor for genotype effects. Default 1.
y_scalar: Scaling factor for phenotype effects. Default 1.
maf: Minor allele frequencies. Default NULL.
coverage: Primary credible-set coverage.
secondary_coverage: Additional credible-set coverages.
signal_cutoff: PIP cutoff for including non-CS variants in top loci.
other_quantities: Optional list carried into each method result.
prior_eff_tol: Tolerance for retaining effects by prior variance.
min_abs_corr: Minimum absolute correlation for credible-set purity.

Value

A list with finemapping_results, top_loci_long, and top_loci. The long table is lossless, with one row per variant-method-coverage-CS membership. The wide table stores one row per variant, method-specific pip_<method> columns, method-specific CS_<coverage>_<method> columns, and model_source.