Replication Data for: Switchgrass Genome Paper

R script containing the code to replicate the results of the switchgrass genome paper. Includes code to: a) run the neural network to assign ecotypes to switchgrass individuals, identified by PLANT_ID's (six character strings that typically begin with J), based on individuals with confidently assigned ecotypes; b) run the discriminant analysis of principle components to assign individuals to the three genetic subpopulations; 1) Run genome-wide association (GWAS); 2) Find gene annotations for top GWAS hits; 3) Make multivariate adaptive shrinkage input dataframes from GWAS hits; 4) Run multivariate adaptive shrinkage; 5) Find heritabilities for GWAS hits and the polygenic background, and do regional heritability mapping for biomass phenotypes.