Genome-Wide Robust Analysis for Biobank Data (GRAB)

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Documentation for package ‘GRAB’ version 0.2.2

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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.