Man pages for jendelman/StageWise
Two-stage analysis of multi-environment trials for genomic selection and GWAS
| blup | BLUP |
| blup_prep | Prepare data for BLUP |
| class_geno-class | S4 class for marker genotype data |
| class_genoD-class | S4 class for marker genotype data with dominance |
| class_prep-class | S4 class to prepare for blup |
| class_var-class | S4 class for variances |
| corr | Trait correlations |
| dominance | Report dominance parameters |
| gain | Genetic gain |
| gwas_threshold | Compute GWAS discovery threshold |
| inbreeding | Genomic inbreeding coefficient |
| manhattan_plot | Create Manhattan plot |
| predict | Predict individual values from marker effects |
| quantile | G matrix quantile |
| read_geno | Read marker genotype data |
| remove_spatialtrend | Remove spatial trend |
| Stage1 | Stage 1 analysis of multi-environment trials |
| Stage2 | Stage 2 analysis of multi-environment trials |
| summary.var | Displays variances and correlations |
| uniplot | Uniplot for multi-location models |
| wheat.data | Genomic prediction from secondary traits in wheat |
