different R function to perform GWAS
The script has been optimized to run with data from Arabidopsis thaliana
gwas.r is a script to run GWAS with a mixed model
The Model uses the fast approximation proposed by Kang et al. 2010 The Null model is solved using the AI algorithm (Gilmour et al. 1995) as it is implemeted in the R library gaston.
plots_gwas.r is a script for plotting the results
emma.r use the emma function (Kang et all. 2008) for the MRLE This is used to fit the full model in the gwas.r script to update the pvalues of the top SNPs.
sim_Y.r is a function to simulate Phenotypes to benchmark and test GWAS approaches. Data need for the simulations are provided in the data section.
ALl data to run GWAS in Arabidopsis can be found at go.uniwue.de/snpextractor see also aragwas.1001genomes.org
Additional sample data for testing purpose can be find in the MTMM repository.