An R script for simple gwassing.
Adapted from the work of researchers at NIAB.
Techniques here were used for MAGIC analysis of awning.
optional arguments: -h, --help show this help message and exit --gFile GFILE Genotype File --pFile PFILE [PFILE ...] Phenotype File --mFile MAP Map File --phenos PHENOS [PHENOS ...] Phenotypes to associate with SNPs --cov [COVS [COVS ...]] Phenotypes to include as mixed effects --outDir OUTDIR Folder to store output in. --noPlots Skip making manhatten plot. --saveInter Whether or not to save intermediate files.