Repository for R scripts used in: Random Forest-based genomic prediction allows selection of barley genotypes from the variety collection for inclusion evaluation in distinctness, uniformity, and stability (DUS) trials.
- script_1_marker_prep.R = Genetic marker quality control.
- script_2_marker_imputation_running.R = Genetic marker imputation using Random Forest.
- script_3_geno_pheno_combine.R = Some phenotypic data quality control and linking up genetic and phenotypic datasets.
- script_4_distances_h2.R = Analyses on population structure and trait heritability.
- script_5_GWAS_slim.R = Association mapping for major genetic loci.
- script_6_prediction_comp.R = Testing different genomic prediction methods.
- script_7_prediction_candidate.R = Genomic selection for subset selection of candidates.
- script_8_similar_var_select_and_plots.R = Subset selection using predicted values and plotting genomic prediction results.