README.Rmd

---
output: github_document
---

<!-- README.md is generated from README.Rmd. Please edit README.Rmd (this file) -->

```{r setup, echo = FALSE, warning = FALSE}
chooseCRANmirror(graphics = FALSE, ind = 1)
knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>"
)
```

# GCA: An R package for genetic connectedness analysis using pedigree and genomic data.  <img src="man/figures/GCA.png" height="200" align="right"/>

## Updates: 

- Maintenance transition: Starting from July, 2024, the `GCA` R package will be maintained by the [AIAOS Lab at the University of Florida](https://github.com/uf-aiaos/). 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. 
```{r, warning = FALSE, message = FALSE, results = 'hide', eval = FALSE}
install.packages("devtools")
```

2. Load the `devtools` package.
```{r, warning = FALSE, results = 'hide', eval = FALSE}
library(devtools)
```

3. Install `GCA` package from GitHub.
```{r, warning = FALSE, results = 'hide', message = FALSE, eval = FALSE}
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.

```{bash, warning = FALSE, results = 'hide', eval = FALSE}
# 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. 
```{r, warning = FALSE, results = 'hide', eval = FALSE}
library(GCA)
```

### Fail to load documentation (e.g., `?GCA`) after reinstalling GCA.
```{r,warning = FALSE, results = 'hide', eval = FALSE}
.rs.restartR() 
```

## Documentation
[Vignette](https://uf-aiaos.github.io/GCA_vignette/GCA.html)

## 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](https://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-021-07414-7)

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