Post-process Fine-mapping Fits

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

postprocessFinemappingFits(
  fits,
  dataX,
  dataY = NULL,
  xScalar = 1,
  yScalar = 1,
  af = NULL,
  coverage = NULL,
  secondaryCoverage = c(0.7, 0.5),
  signalCutoff = 0.1,
  otherQuantities = NULL,
  region = NULL,
  priorEffTol = 1e-09,
  minAbsCorr = 0.8,
  medianAbsCorr = NULL,
  csInput = NULL,
  conditionIdx = NULL,
  trim = TRUE,
  fullFit = FALSE,
  fullFitAlphaOnly = TRUE,
  includeAllCs = FALSE
)

Arguments

fits

Named list of fine-mapping fits. Names define method identity, for example susie, susieInf, susieRss, mvsusie, or fsusie.

dataX

Genotype matrix, LD/correlation matrix, or other method-specific input used for credible-set purity and correlations.

dataY

Phenotype vector/matrix or summary statistics. Default NULL.

xScalar

Scaling factor for genotype effects. Default 1.

yScalar

Scaling factor for phenotype effects. Default 1.

af

Effect-allele frequencies (exported as the af column; never MAF). Default NULL.

coverage

Primary credible-set coverage.

secondaryCoverage

Additional credible-set coverages.

signalCutoff

PIP cutoff for including non-CS variants in top loci.

otherQuantities

Optional list carried into each method result.

priorEffTol

Tolerance for retaining effects by prior variance.

minAbsCorr

Minimum absolute correlation for credible-set purity.

Value

A list with finemappingResults (per-method post-processed objects, each carrying a trimmed fit and method-specific intermediates) and a single unified top_loci table in the fixed 22-column shape (see the internal buildTopLoci). Per-method contributions are row-bound into top_loci by an outer method for-loop.