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.

Release v0.2.2 (2025-08-01)

The following notes summarize the main changes from v0.2.0 to v0.2.2.

Resolved all issues raised by the CRAN manual review to meet publication requirements, including:

• Updated the Description field in DESCRIPTION to a single-paragraph summary with relevant references
• Added a @return section to the documentation of all exported functions where absent
• Replaced all print() and cat() statements with message() to allow users to suppress output if desired.
• Removed code that set specific random seeds inside functions
• Redirect example output files to the R session’s tempdir() to avoid side effects on the user’s file system.

Increased the number of markers (which was decreased from 10k to 1k to minimize package size and running time) in the example dataset from 1k to 1.1k to ensure the number of markers exceeds the number of subjects.

Moved inst/docker back to the project root and excluded it from the package build.

Relesae v0.2.0 (2025-07-17)

Add a new method, WtCoxG, and bump version to 0.2.0.

We reorganized the Depends, Imports, Suggests and LinkingTo fields in the DESCRIPTION file for clarity and correctness. Additionally, we consolidated Makevars and Makevars.win into a single Makevars file for simplified build configuration.

In previous versions, GRAB automatically imported all functions and objects from its dependent packages and exported all package objects to the user’s workspace. We have updated the NAMESPACE file so that GRAB now only imports specific functions as needed from dependencies and only exports user-facing functions. This results in a cleaner namespace and avoids cluttering the user’s environment with unnecessary objects.

We no longer include a copy of GCTA program within the package. Instead, users have to specify the path of the GCTA executable on their system using gcta64File parameter when calling getTempFilesFullGRM(). We have successfully tested getTempFilesFullGRM() with GCTA v1.94.4 on Windows. Despite previous documentation indicating Linux-only support, this function works on Windows systems as well.

We have tested and debugged all examples included in the function help files, and verified that they execute correctly. We have minimized the package size and example running time. Additionally, we have made all necessary changes to ensure the package complies with CRAN policies and requirements, passing R CMD check --as-cran with no ERROR or WARNING, and as few NOTE as possible.

The old version 0.1.2 can be found in branch release/v0.1.2. This branch will serve as an archive and will no longer be actively maintained.