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GRAB

GRAB is an R package that provides a comprehensivesuite of GWAS methods for biobank-scale data. For detailed instructions,see theGRABmanual page.

Version 0.1.2 (the last version before v0.2.0 and prior to June 2025)is archived in branchrelease/v0.1.2.

Installation

GRAB is an R package, with part of its code written in C++ forimproved performance. GRAB can be installed on Linux, Windows, or macOSvia CRAN, Conda, or from source code.

Install via CRAN

Install GRAB from CRAN in your R console:

install.packages("GRAB",dependencies =TRUE)

Install via Conda

Install GRAB in a new Conda environment namedgrab_envfrom theconda-forge channel:

conda create-n grab_env-c conda-forge r-grab r-skat r-dbplyr r-tidyr r-r.utils

Quick tutorial

Here is a quick tutorial for GWAS of a time-to-event trait usingSPAmix.

Step 1: fit a null model

library(GRAB)PhenoFile<-system.file("extdata","simuPHENO.txt",package ="GRAB")PhenoData<- data.table::fread(PhenoFile,header =TRUE)obj.SPAmix<-GRAB.NullModel(  survival::Surv(SurvTime, SurvEvent)~ AGE+ GENDER+ PC1+ PC2,data = PhenoData,subjIDcol ="IID",method ="SPAmix",traitType ="time-to-event",control =list(PC_columns ="PC1,PC2"))

Step 2: conduct score test

GenoFile<-system.file("extdata","simuPLINK.bed",package ="GRAB")OutputFile<-file.path(tempdir(),"Results_SPAmix.txt")GRAB.Marker(obj.SPAmix,GenoFile = GenoFile,OutputFile = OutputFile)data.table::fread(OutputFile)