GCA: An R package for genetic connectedness analysis using pedigree and genomic data.

Updates:

• Maintenance transition: Starting from July, 2024, the GCA R package will be maintained by the AIAOS Lab at the University of Florida. The AIAOS Lab will handle all future maintenance, updates, and support for the package.

Installation

GCA is currently available on GitHub and can be installed using devtools package:

1. Install devtools package from CRAN.

install.packages("devtools")

2. Load the devtools package.

library(devtools)

3. Install GCA package from GitHub.

install_github('uf-aiaos/GCA')

Note: For Apple Silicon (ARM64) users, if you encounter the error Could not find tools necessary to compile a package, it can be fixed using the following command.

# Check the version of gcc installed by homebrew
ls /opt/homebrew/bin/gcc* 

# Create a symlink `gcc` under /usr/local/bin/ and point to the gcc installed by Homebrew (gcc-14 in this case). 
sudo ln -s /opt/homebrew/bin/gcc-14 /usr/local/bin/gcc

# Restart the terminal and then install the package using `install_github('uf-aiaos/GCA')`.

4. Load GCA package.

library(GCA)

Fail to load documentation (e.g., ?GCA) after reinstalling GCA.

.rs.restartR() 

Documentation

Vignette

Contact information and help

• Haipeng Yu (haipengyu@ufl.edu)

Reference

Haipeng Yu and Gota Morota. GCA: An R package for genetic connectedness analysis using pedigree and genomic data. BMC Genomics, 2021. 10.1186/s12864-021-07414-7

License

This project is primarily licensed under the GNU General Public License version 3 (GPLv3).