The hardware and bandwidth for this mirror is donated by dogado GmbH, the Webhosting and Full Service-Cloud Provider. Check out our Wordpress Tutorial.
If you wish to report a bug, or if you are interested in having us mirror your free-software or open-source project, please feel free to contact us at mirror[@]dogado.de.

GRAB

GRAB is an R package that provides a comprehensive suite of GWAS methods for biobank-scale data. For detailed instructions, see the GRAB manual page.

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

Installation

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

Install via CRAN

Install GRAB from CRAN in your R console:

install.packages("GRAB")

Install via Conda

Install GRAB in a new Conda environment named grab_env from the conda-forge channel:

conda create -n grab_env -c conda-forge r-grab

Quick tutorial

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

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,
  subjData = 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)

These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.
Health stats visible at Monitor.