R/mvwgaim: An R package for efficient multi-(environment/variate/treatment) whole genome QTL analysis

Authors: Julian Taylor & Ari Verbyla

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

R/mvwgaim is a multi-(environment/variate/treatment) whole genome average interval mapping R package that implements the multi-environment wgaim algorithm derived in Verbyla et al. (2007, 2012). The packages main QTL 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 mvwgaim using

devtools::install_github("DrJ001/mvwgaim")

Getting Started

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

References

Verbyla, A.P., Cullis, B.R. & Thompson, R. (2007) The analysis of QTL by simultaneous use of the of the full linkage map. Theoretical and Applied Genetics, 116, 95-111.

Verbyla, A. P., & Cullis, B. R. (2012) Multivariate whole genome average interval mapping: QTL analysis for multiple traits and/or environments. Theoretical and applied genetics 125, 933-953.