# Genome-Wide Robust Analysis for Biobank Data (GRAB)

## Documentation for package ‘GRAB’ version 0.2.1

- DESCRIPTION file.

## Help Pages

Batcheffect.Test | Test for batch effect
CCT | An analytical p-value combination method using the Cauchy distribution
checkIfSampleIDsExist | Check if sample identifiers are stored in a BGEN file
getDenseGRM | Suppose that a dense GRM is Phi and input is bVec, return Phi * bVec (only for developers)
getSampleIDsFromBGEN | Get sample identifiers from BGEN file
getSparseGRM | Make a 'SparseGRMFile' for 'GRAB.NullModel'.
getTempFilesFullGRM | Make temporary files to be passed to function 'getSparseGRM'.
getVersionFromBGEN | Get version information from BGEN file
GRAB.getGenoInfo | Get allele frequency and missing rate information from genotype data
GRAB.makePlink | Make PLINK files using a numeric R matrix
GRAB.Marker | Conduct marker-level genetic association testing
GRAB.NullModel | Fit a null model to estimate parameters and residuals
GRAB.POLMM | POLMM method in GRAB package
GRAB.ReadGeno | Read in genotype data
GRAB.Region | Conduct region-level genetic association testing
GRAB.SAGELD | SAGELD method in GRAB package
GRAB.SimubVec | GRAB: simulate random effect (i.e. bVec) based on family structure
GRAB.SimuGMat | Simulate an R matrix of genotype data
GRAB.SimuGMatFromGenoFile | GRAB: simulate genotype matrix based on family structure
GRAB.SimuPheno | Simulate phenotype using linear predictor 'eta'
GRAB.SPACox | SPACox method in GRAB package
GRAB.SPAGRM | SPAGRM method in GRAB package
GRAB.SPAmix | SPAmix method in GRAB package
GRAB.WtCoxG | WtCoxG method in GRAB package
handleFormula | handle a formula (used in GRAB.NullModel function)
makeGroup | A lower function to make groups based on phenotype
SAGELD.NullModel | Fit a SAGELD Null Model
setDenseGRM | Set up a dense GRM (only for developers)
SPAGRM.NullModel | Fit a SPAGRM Null Model
TestforBatchEffect | Quality control to check batch effect between study cohort and reference population.