The goal of BREADR is to provide an easy-to-use method for estimating degrees of relatedness (up to the second degree) for extremely low-coverage data. BREADR also allows users to quantify and visualise the level of confidence in the estimated degrees of relatedness.
The method requires Eigenstrat files (an ind, geno and snp file) to begin, allowing the user to account for DNA deamination when genotyping their data.
Further information can be found at the BREADR website.
Installation
To install, you can use the usual
install.packages("BREADR")You can install the development version of BREADR from GitHub with:
# install.packages("remotes")
remotes::install_github("jonotuke/BREADR")Also to ensure that BREADR install correctly, we suggest installing the following packages
- Matrix,
- data.table,
- dplyr,
- forcats,
- ggplot2,
- ggpubr,
- grDevices,
- magrittr,
- MASS,
- matrixStats,
- purrr,
- readr,
- stringr and
- tibble.
Contributing to BREADR
Please note that BREADR is work in progress! If you are interested in the project and want to know more please feel free to contact Jono Tuke (simon.tuke@adelaide.edu.au). If you find a bug or would like to see new or improved features, please open an issue on the GitHub repository.