Package: GRAB 0.2.2

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

Provides a comprehensive suite of genome-wide association study (GWAS) methods specifically designed for biobank-scale data. The package offers computationally efficient and robust association tests for time-to-event traits (e.g., Bi et al., 2020 <doi:10.1016/j.ajhg.2020.06.003>), ordinal categorical traits (e.g., Bi et al., 2021 <doi:10.1016/j.ajhg.2021.03.019>), and longitudinal traits (Xu et al., 2025 <doi:10.1038/s41467-025-56669-1>). Additionally, it includes functions for simulating genotype and phenotype data to support research and method development.

Authors:Wenjian Bi [aut], Wei Zhou [aut], Rounak Dey [aut], Zhangchen Zhao [aut], Seunggeun Lee [aut], Woody Miao [cre]

GRAB_0.2.2.tar.gz
GRAB_0.2.2.zip(r-4.7)GRAB_0.2.2.zip(r-4.6)GRAB_0.2.2.zip(r-4.5)
GRAB_0.2.2.tgz(r-4.6-x86_64)GRAB_0.2.2.tgz(r-4.6-arm64)GRAB_0.2.2.tgz(r-4.5-x86_64)GRAB_0.2.2.tgz(r-4.5-arm64)
GRAB_0.2.2.tar.gz(r-4.7-arm64)GRAB_0.2.2.tar.gz(r-4.7-x86_64)GRAB_0.2.2.tar.gz(r-4.6-arm64)GRAB_0.2.2.tar.gz(r-4.6-x86_64)
GRAB_0.2.2.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
GRAB/json (API)

# Install 'GRAB' in R:
install.packages('GRAB', repos = c('https://woodymiao.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/woodymiao/grab/issues

Uses libs:
  • zlib– Compression library
  • openblas– Optimized BLAS
  • c++– GNU Standard C++ Library v3

On CRAN:

Conda:

zlibopenblascpp

4.85 score 142 scripts 160 downloads 29 exports 47 dependencies

Last updated from:b83c948397. Checks:13 OK. Indexed: yes.

TargetResultTimeFilesSyslog
linux-devel-arm64OK264
linux-devel-x86_64OK241
source / vignettesOK264
linux-release-arm64OK287
linux-release-x86_64OK248
macos-release-arm64OK273
macos-release-x86_64OK345
macos-oldrel-arm64OK199
macos-oldrel-x86_64OK643
windows-develOK290
windows-releaseOK298
windows-oldrelOK261
wasm-releaseOK189

Exports:CCTcheckIfSampleIDsExistgetDenseGRMgetSampleIDsFromBGENgetSparseGRMgetTempFilesFullGRMgetVersionFromBGENGRAB.getGenoInfoGRAB.makePlinkGRAB.MarkerGRAB.NullModelGRAB.POLMMGRAB.ReadGenoGRAB.RegionGRAB.SAGELDGRAB.SimubVecGRAB.SimuGMatGRAB.SimuGMatFromGenoFileGRAB.SimuPhenoGRAB.SPACoxGRAB.SPAGRMGRAB.SPAmixGRAB.WtCoxGhandleFormulamakeGroupSAGELD.NullModelsetDenseGRMSPAGRM.NullModelTestforBatchEffect

Dependencies:BHbitbit64blobbootcachemclicpp11data.tableDBIdplyrfastmapgenericsglueigraphlatticelifecyclelme4magrittrMASSMatrixmemoiseminqamvtnormnlmenloptrnumDerivordinalpillarpkgconfigR6rbibutilsRcppRcppArmadilloRcppEigenRcppParallelRdpackreformulasrlangRSQLitesurvivaltibbletidyselectucminfutf8vctrswithr

Readme and manuals

Help Manual

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