Builds the SPAGRM null model object using subject residuals, sparse GRM, and pairwise IBD estimates, detecting residual outliers and constructing family-level graph structures for downstream saddlepoint marker tests.
SPAGRM.NullModel(
ResidMatFile,
SparseGRMFile,
PairwiseIBDFile,
control = list(MaxQuantile = 0.75, MinQuantile = 0.25, OutlierRatio = 1.5,
ControlOutlier = TRUE, MaxNuminFam = 5, MAF_interval = c(1e-04, 5e-04, 0.001, 0.005,
0.01, 0.05, 0.1, 0.2, 0.3, 0.4, 0.5))
)A list of class "SPAGRM_NULL_Model" with elements:
Numeric vector of residuals used in analysis.
Character vector of subject IDs (length = N).
Number of subjects.
Residuals of unrelated outlier subjects.
Sum of quadratic form Resid' * GRM * Resid for all subjects.
Aggregate contribution from two-subject outlier families.
Sum of residuals for non-outlier unrelated subjects.
Quadratic form contribution for non-outlier unrelated subjects.
List with per two-member family residual/Rho info.
List with Chow–Liu tree structures and standardized scores for larger families.
Vector of MAF breakpoints used in tree construction.
Data frame or file path with columns SubjID, Resid.
File path to sparse GRM (tab-delimited: ID1, ID2, Value).
File path to pairwise IBD table (ID1, ID2, pa, pb, pc).
List of options controlling outlier handling and family
decomposition (see checkControl.SPAGRM.NullModel).