This repository present a set of modules for analysis of data from multi-environment trials using genotype (SNP) and environmental covariates. The methods presented here are largley based on Jarquin et al. (2014). The project has ben funded by Arvalis (PI: G. de los Campos).
Contact: Gustavo de los Campos [ gdeloscampos@gmail.com ] & Marco Lopez-Cruz [ malctony@hotmail.com ]
The modules are based on R (>=3.1.0 download). Before you start, be sure to install the packages BGLR and lme4.
install.packages("BGLR",repos="http://cran.r-project.org")
install.packages("lme4",repos="http://cran.r-project.org")- Module 0: Preparing inputs
- Module 1: Variance Components (lmer)
- Module 2: Variance Components (BGLR)
- Module 3: Structure of genotypes and of environments
- Module 4: Genomic Regressions using BGLR
- Module 5: Cross-validation
- Module 6: Splines with lme4
- Module 7: Splines with BGLR (includes markers)
- Moudle 8: Simulation Manuscript