fitNullModel.WtCoxG: Fit weighted Cox null model with outlier handling and batch-effect QC

Description

Fits a weighted Cox model using case/control weighting based on reference prevalence and identifies residual outliers for SPA testing. Optionally performs batch-effect QC by cross-referencing external allele frequencies.

Usage

fitNullModel.WtCoxG(
  response,
  designMat,
  subjData,
  control,
  data,
  GenoFile,
  GenoFileIndex,
  SparseGRMFile,
  SurvTimeColumn,
  IndicatorColumn,
  ...
)

Value

A list of class "WtCoxG_NULL_Model" with elements:

mresid: Martingale residuals from weighted Cox model.
Cova: Design matrix used in the null model (n x p).
yVec: Event indicator extracted from Surv.
weight: Observation weights derived from reference prevalence.
RefPrevalence: Reference prevalence used to define weights.
N: Number of subjects.
outLierList: Lists indices (0-based) and residual subsets for SPA.
control: Copy of control options used.
mergeGenoInfo: QC-derived marker metadata for batch-effect testing (if run).
subjData: Character vector of subject IDs.

Arguments

response: survival::Surv response (time-to-event). Residuals are not supported here.
designMat: Numeric matrix (n x p) of covariates.
subjData: Character vector of subject IDs aligned with rows of designMat.
control: List with fields such as OutlierRatio.
data: Data frame used for optional batch-effect QC.
GenoFile: Character. PLINK prefix (without extension) used when sampling markers for QC.
GenoFileIndex: Character. Path to an index file used in QC workflow.
SparseGRMFile: Character. Path to sparse GRM used in QC workflow.
SurvTimeColumn: Character. Column name in data containing survival time.
IndicatorColumn: Character. Column name in data containing event indicator (0/1).
...: Optional named parameters forwarded to QC (e.g., RefAfFile).