R/GWASReml: An R package for multi-(environment/variate/treatment) GWAS analysis

Authors: Julian Taylor

This is the public facing GitHub repository version of the R package GWASReml.

R/GWASReml is a multi-(environment/variate/treatment) genome wide association analysis R package that allows users to flexibly scan markers within one or more chromosomes. The package allows various markers scanning approaches including the well established approach outlined in Malosetti et al. (2013). The main analysis function uses ASReml-R V4 for its core linear mixed modelling. To use full functionality of the package users will require a valid license for ASReml-R V4 and this can be obtained from https://www.vsni.co.uk/software/asreml-r.

To install the package from GitHub you will need to do the following:

1. Install the devtools package. Do this by invoking R and then typing

install.packages("devtools")

2. Install GWASreml using

devtools::install_github("DrJ001/GWASReml")

Getting Started

For a quick but complete introduction of the functionality of the package please see the extensive help files of the package.

References

Malosetti,M., Ribaut,J.-M., and van Eeuwijk,F. A. (2013) The statistical analysis of multi-environment data: modeling genotype-by-environment interaction and its genetic basis. Frontiers in physiology, 4, 44.