Man pages for jendelman/GWASpoly
Genome-wide Association Studies for Autopolyploids
| fit.QTL | Test markers as QTL under backward elimination |
| get.QTL | Extract significant QTL |
| GWASpoly | Compute marker significance scores |
| GWASpoly.data-class | S4 class with genotype and phenotype data |
| GWASpoly.fitted-class | S4 class with results from genome-wide scan |
| GWASpoly.K-class | S4 class with genotypes, phenotypes, and polygenic covariance |
| GWASpoly.thresh-class | S4 class with results from genome-wide scan and detection... |
| Keff | Effective number of markers |
| LD.plot | Plot LD vs distance |
| manhattan.plot | Create Manhattan plot |
| qq.plot | Quantile-Quantile (QQ) Plot |
| read.GWASpoly | Read in marker and phenotype data |
| set.K | Set covariance matrix for polygenic effect |
| set.params | Set parameters |
| set.threshold | Set the significance threshold |
| VCF2dosage | Convert VCF to dosage file |
| write.GWASpoly | Write results to file |
