Overview: this page provides a comprehensive reference for all parameters and options available in GWAS functions, including GRAB.NullModel(), SPAGRM.NullModel(), GRAB.Marker(), and GRAB.Region().

`GRAB.NullModel`

Required Parameters

Parameter	Type	Description
`formula`	formula	Formula with response variable(s) on left and covariates on right. Intercept added automatically. For SPAmix with `traitType="Residual"`, multiple response variables separated by `+` are supported.
`data`	data.frame	Data frame containing response variables and covariates. Missing values coded as `NA`.
`method`	character	Method to use: `"POLMM"`, `"SPACox"`, `"SPAmix"`, `"SPAGRM"`, or `"WtCoxG"`.
`traitType`	character	Trait type: `"ordinal"`, `"time-to-event"`, or `"Residual"`.
`GenoFile`¹	character	Path to genotype file. Required for POLMM and WtCoxG. Extensions: `.bed` (PLINK) or `.bgen` (BGEN v1.2 with 8-bit).
`subjIDcol`²	character	Column name in `data` containing subject IDs.
`subjData`²	character or numeric vector	Vector of subject IDs aligned with the rows of `data`.
`RefAfFile`³	character	Path to reference allele frequency file with columns: `CHROM`, `POS`, `ID`, `REF`, `ALT`, `AF_ref`, `AN_ref`.
`RefPrevalence`³	numeric	Population-level disease prevalence for weighting. Range: (0, 0.5).

¹ GenoFile is required only for POLMM and WtCoxG.

² Exactly one of subjIDcol and subjData must be provided.

³ RefAfFile and RefPrevalence are WtCoxG specific.

Optional Parameters

Parameter	Type	Default	Description
`GenoFileIndex`	character vector	`NULL`	Index files for genotype file. Auto-detected if `NULL`. For PLINK: `c("prefix.bim", "prefix.fam")`. For BGEN: `c("prefix.bgen.bgi", "prefix.sample")`.
`SparseGRMFile`	character	`NULL`	Path to sparse GRM file. Tab-delimited with 3 columns: `ID1`, `ID2`, `Value`.
`control`	list	`NULL`	Control parameters. See below; optional unless marked as required.

Control Parameters (optional unless marked as required)

POLMM Control Parameters

Parameter	Type	Default	Description
`memoryChunk`	numeric	2	Memory chunk size for computation (GB); must be > 0.
`seed`	integer	-1	Random seed (-1 = no seed set).
`tracenrun`	integer	30	Number of runs for trace calculation; must be > 0.
`maxiter`	integer	100	Maximum iterations for model fitting; must be > 0.
`tolBeta`	numeric	0.001	Convergence tolerance for beta estimates; must be > 0.
`tolTau`	numeric	0.002	Convergence tolerance for tau estimates; must be > 0.
`tau`	numeric	0.2	Initial variance component value; must be > 0.
`maxiterPCG`	integer	100	Maximum iterations for preconditioned conjugate gradient (PCG); must be > 0.
`tolPCG`	numeric	1e-6	Tolerance for PCG convergence; must be > 0.
`showInfo`	logical	`FALSE`	Print PCG iteration information for debugging.
`maxiterEps`	integer	100	Maximum iterations for epsilon estimation; must be > 0.
`tolEps`	numeric	1e-10	Tolerance for epsilon estimation; must be > 0.
`minMafVarRatio`	numeric	0.1	Minimum MAF for variance ratio estimation; range [0, 0.5].
`maxMissingVarRatio`	numeric	0.1	Maximum missing rate for variance ratio estimation; range [0, 1].
`nSNPsVarRatio`	integer	20	Number of SNPs for variance ratio estimation; must be > 0.
`CVcutoff`	numeric	0.0025	Coefficient of variation cutoff; must be > 0.
`grainSize`	integer	1	Grain size for parallel processing; must be > 0.
`minMafGRM`	numeric	0.01	Minimum MAF for GRM construction; range [0, 0.5].
`maxMissingGRM`	numeric	0.1	Maximum missing rate for GRM construction; range [0, 1].

SPACox Control Parameters

Parameter	Type	Default	Description
`range`	numeric vector	`c(-100, 100)`	Range for SPA grid; must be symmetric (i.e., `range[2] = -range[1]`).
`length.out`	integer	10000	Number of grid points for SPA approximation; must be > 1000.

SPAmix Control Parameters

Parameter	Type	Default	Description
`PC_columns`	character	Required	Comma-separated column names of principal components (e.g., `"PC1,PC2,PC3"`). Must be in formula.
`OutlierRatio`	numeric	1.5	IQR multiplier for outlier detection; must be > 0. Outliers defined as outside `[Q1 - r×IQR, Q3 + r×IQR]`.

WtCoxG Control Parameters

Parameter	Type	Default	Description
`OutlierRatio`	numeric	1.5	IQR multiplier for outlier detection; must be > 0.

`SPAGRM.NullModel`

Required Parameters

Parameter	Type	Description
`ResidMatFile`	data.frame or character	Data frame or file path with columns `SubjID`, `Resid`. Tab/space-delimited if file.
`SparseGRMFile`	character	Path to sparse GRM file. Tab-delimited with 3 columns: `ID1`, `ID2`, `Value`.
`PairwiseIBDFile`	character	Path to pairwise IBD file. Tab-delimited with 5 columns: `ID1`, `ID2`, `pa`, `pb`, `pc`.

Control Parameters (optional)

Parameter	Type	Default	Description
`MaxQuantile`	numeric	0.75	Upper quantile for outlier detection; range [0, 1].
`MinQuantile`	numeric	0.25	Lower quantile for outlier detection; range [0, 1].
`OutlierRatio`	numeric	1.5	IQR multiplier for outlier bounds; must be > 0.
`ControlOutlier`	logical	`TRUE`	Adjust ratio to keep outliers < 5%. Set `FALSE` for higher accuracy.
`MaxNuminFam`	integer	5	Maximum family size for graph decomposition; must be ≥ 2.
`MAF_interval`	numeric vector	`c(0.0001, 0.0005, 0.001, 0.005, 0.01, 0.05, 0.1, 0.2, 0.3, 0.4, 0.5)`	MAF breakpoints for Chow-Liu tree construction; must be in increasing order.

`GRAB.Marker`

Required Parameters

Parameter	Type	Description
`objNull`	S3 object	Null model from `GRAB.NullModel()`, `SPAGRM.NullModel()`, or `SAGELD.NullModel()`. Supported classes: `POLMM_NULL_Model`, `SPACox_NULL_Model`, `SPAmix_NULL_Model`, `SPAGRM_NULL_Model`, `SAGELD_NULL_Model`, `WtCoxG_NULL_Model`.
`GenoFile`	character	Path to genotype file. Extensions: `.bed` (PLINK) or `.bgen` (BGEN v1.2).
`OutputFile`	character	Path for saving association results.

Optional Parameters

Parameter	Type	Default	Description
`GenoFileIndex`	character vector	`NULL`	Index files for genotype file. Auto-detected if `NULL`.
`OutputFileIndex`	character	`NULL`	Progress tracking file path. Default: `paste0(OutputFile, ".index")`. Enables restart if interrupted.
`control`	list	`NULL`	Control parameters (see below).

Control Parameters (optional)

Common Control Parameters

Parameter	Type	Default	Description
`AlleleOrder`	character	`NULL`	Allele order in genotype file: `"ref-first"`, `"alt-first"`, or `NULL`. Default: `"alt-first"` for BGEN, `"ref-first"` for PLINK.
`impute_method`	character	`"mean"`	Imputation method for missing genotypes: `"mean"`, `"minor"`, or `"drop"`.
`missing_cutoff`	numeric	0.15	Exclude markers with missing rate above this threshold; range [0, 0.5].
`min_maf_marker`	numeric	0.001	Exclude markers with MAF below this threshold; range [0, 0.1].
`min_mac_marker`	numeric	20	Exclude markers with MAC below this threshold; range [0, 100].
`nMarkersEachChunk`	integer	10000	Number of markers processed per chunk; range [1000, 100000].
`SPA_Cutoff`	numeric	2	Z-score cutoff for saddlepoint approximation; must be > 0. SPA used when z-score > cutoff.
`AllMarkers`	logical	`TRUE`	Analyze all markers. Automatically `FALSE` if include/exclude files provided.
`IDsToIncludeFile`¹	character	`NULL`	File with marker IDs to include (one per line).
`RangesToIncludeFile`¹	character	`NULL`	File with genomic ranges to include. Can combine with `IDsToIncludeFile` (union used).
`IDsToExcludeFile`¹	character	`NULL`	File with marker IDs to exclude (one per line).
`RangesToExcludeFile`¹	character	`NULL`	File with genomic ranges to exclude. Can combine with `IDsToExcludeFile` (union excluded).

¹ Cannot use both include and exclude files simultaneously.

POLMM Control Parameters

Parameter	Type	Default	Description
`ifOutGroup`	logical	`FALSE`	Output group-specific statistics (allele frequency, counts, sample size per ordinal category). Adds columns: `AltFreqInGroup.`, `AltCountsInGroup.`, `nSamplesInGroup.*`.

SPACox Control Parameters

Parameter	Type	Default	Description
`pVal_covaAdj_Cutoff`	numeric	5e-05	P-value cutoff for covariate adjustment.

SPAmix Control Parameters

Parameter	Type	Default	Description
`dosage_option`	character	`"rounding_first"`	Dosage handling method: `"rounding_first"` or `"rounding_last"`.

SPAGRM Control Parameters

Parameter	Type	Default	Description
`zeta`	numeric	0	SPA moment approximation parameter.
`tol`	numeric	1e-5	Numerical tolerance for SPA convergence.

WtCoxG Control Parameters

Parameter	Type	Default	Description
`cutoff`	numeric	0.1	Batch effect test p-value cutoff; range [0, 1]. Variants with p-value below cutoff excluded from association testing.

`GRAB.Region`

Required Parameters

Parameter	Type	Description
`objNull`	S3 object	Null model from `GRAB.NullModel()`. Currently supports `POLMM_NULL_Model`.
`GenoFile`	character	Path to genotype file (PLINK or BGEN).
`OutputFile`	character	Path for saving region-based results.
`GroupFile`	character	Path to region definition file with region-marker mappings and annotations. Tab-separated with 2-3 columns per region.

Optional Parameters

Parameter	Type	Default	Description
`GenoFileIndex`	character vector	`NULL`	Index files. Auto-detected if `NULL`.
`OutputFileIndex`	character	`NULL`	Progress tracking file. Default: `paste0(OutputFile, ".index")`.
`SparseGRMFile`	character	`NULL`	Path to sparse GRM file.
`MaxMAFVec`	character	`"0.01,0.001,0.0005"`	Comma-separated MAF cutoffs for variant inclusion.
`annoVec`	character	`"lof,lof:missense,lof:missense:synonymous"`	Comma-separated annotation groups for analysis.
`control`	list	`NULL`	Control parameters (see below).

Control Parameters (optional)

Common Control Parameters

Parameter	Type	Default	Description
`impute_method`	character	`"minor"`	Imputation method for missing genotypes: `"mean"`, `"minor"`, or `"drop"`.
`missing_cutoff`	numeric	0.15	Exclude markers with missing rate above threshold; range [0, 0.5].
`min_mac_region`	numeric	5	Minimum MAC threshold (≥ 0). Markers with MAC < threshold treated as ultra-rare.
`max_markers_region`	integer	100	Maximum markers allowed per region; must be ≥ 50.
`r.corr`	numeric vector	`c(0, 0.1^2, 0.2^2, 0.3^2, 0.4^2, 0.5^2, 0.5, 1)`	Rho parameters for SKAT-O test; each value in [0, 1].
`weights.beta`	numeric vector	`c(1, 25)`	Beta distribution parameters for variant weights; length 2, each ≥ 0.
`min_nMarker`	integer	3	Minimum markers required for region analysis; must be > 0.
`SPA_Cutoff`	numeric	2	Z-score cutoff for SPA; must be > 0.

POLMM Control Parameters

Parameter	Type	Default	Description
`showInfo`	logical	`FALSE`	Print PCG iteration information for debugging.
`tolPCG`	numeric	0.001	Tolerance for PCG in region testing.
`maxiterPCG`	integer	100	Maximum PCG iterations in region testing.