SAGELD.NullModel: Construct SAGELD/GALLOP null model from a mixed-effects fit

Description

Builds the SAGELD (or GALLOP) null model from a fitted mixed-effects model and relatedness inputs. Extracts variance components, forms the penalization matrix, derives residual summaries, and (for SAGELD) integrates sparse GRM and pairwise IBD to prepare graph-based components for marker testing.

Usage

SAGELD.NullModel(
  NullModel,
  UsedMethod = "SAGELD",
  PlinkFile,
  SparseGRMFile,
  PairwiseIBDFile,
  PvalueCutoff = 0.001,
  control = list()
)

Value

A list of class "SAGELD_NULL_Model" with elements:

subjData: Character vector of subject IDs.
N: Number of subjects.
Method: Method label: "SAGELD" or "GALLOP".
XTs: Per-subject sums for crossprod(X, G) terms.
SS: Per-subject Rot %*% Si matrices for random effects.
AtS: Per-subject cross-products used in variance assembly.
Q: Fixed-effect precision matrix (p x p).
A21: Block matrix linking random and fixed effects.
TTs: Per-subject sums for crossprod(G).
Tys: Per-subject sums for crossprod(G, y).
sol: Fixed-effects solution vector.
blups: Random-effects BLUPs per subject.
sig: Scale parameter extracted from VarCorr.
Resid: Residuals used in SAGELD testing.
Resid_G: Genetic component residuals.
Resid_GxE: GxE component residuals.
Resid_E: Environmental component residuals.
Resid.unrelated.outliers: Residuals for unrelated outlier subjects.
Resid.unrelated.outliers_G: G residuals for unrelated outliers.
Resid.unrelated.outliers_GxE: GxE residuals for unrelated outliers.
R_GRM_R: Quadratic form Resid' * GRM * Resid (all subjects).
R_GRM_R_G: Quadratic form for G residuals.
R_GRM_R_GxE: Quadratic form for GxE residuals.
R_GRM_R_G_GxE: Cross-term quadratic form between G and GxE.
R_GRM_R_E: Quadratic form for E residuals.
R_GRM_R_TwoSubjOutlier: Contribution from two-subject outlier families.
R_GRM_R_TwoSubjOutlier_G: Two-subject outlier contribution (G).
R_GRM_R_TwoSubjOutlier_GxE: Two-subject outlier contribution (GxE).
R_GRM_R_TwoSubjOutlier_G_GxE: Two-subject outlier cross-term (G,GxE).
sum_R_nonOutlier: Sum of residuals for non-outlier unrelated subjects.
sum_R_nonOutlier_G: Sum of G residuals for non-outlier unrelated subjects.
sum_R_nonOutlier_GxE: Sum of GxE residuals for non-outlier unrelated subjects.
R_GRM_R_nonOutlier: Quadratic form for non-outlier unrelated subjects.
R_GRM_R_nonOutlier_G: Quadratic form for G (non-outlier unrelated).
R_GRM_R_nonOutlier_GxE: Quadratic form for GxE (non-outlier unrelated).
R_GRM_R_nonOutlier_G_GxE: Cross-term for G/GxE (non-outlier unrelated).
TwoSubj_list: Per-family lists for N=2 outlier families.
ThreeSubj_list: CLT and standardized scores for larger families.
MAF_interval: MAF breakpoints used in CLT construction.
zScoreE_cutoff: Z-score threshold for E used in screening.

Arguments

NullModel: A fitted model from lme4 (class merMod) or glmmTMB with a subject-specific random intercept (e.g., (1|ID)).
UsedMethod: Character; either "SAGELD" (default) or "GALLOP".
PlinkFile: Character. PLINK prefix (without extension) used to sample common markers for estimating the lambda parameter.
SparseGRMFile: Character. Path to sparse GRM file produced by getSparseGRM().
PairwiseIBDFile: Character. Path to pairwise IBD file produced by getPairwiseIBD().
PvalueCutoff: Numeric p-value threshold for screening gene–environment association when estimating \(\lambda\).
control: List of options (forwarded to internal checks; see checkControl.SAGELD.NullModel).