Man pages for mppR
Multi-Parent Population QTL Analysis
| create.mppData | Create a multi-parent population data object |
| CV_partition | Cross validation partition |
| design_connectivity | Connected parts of a MPP design |
| IBD.mppData | IBD coding for 'mppData' objects |
| IBS.mppData | IBS coding for 'mppData' objects |
| inc_mat_QTL | QTL incidence matrix |
| mpp_back_elim | Backward elimination on QTL candidates |
| mpp_CIM | MPP Composite Interval Mapping |
| mpp_CV | MPP cross-validation |
| mppData | Complete 'mppData' object |
| mppData_add_pheno | Add new phenotypic values to a mppData object |
| mppData_GE | Example 'mppData' object |
| mppData_init | 'mppData' object with raw data |
| mppData_mdf_pheno | Modify the phenotypic values of a mppData object |
| mpp_forward | MPP QTL analysis using forward regression |
| mppGE_CIM | MPP GxE Composite Interval Mapping |
| mppGE_proc | MPP GxE QTL analysis |
| mppGE_SIM | MPP GxE Simple Interval Mapping |
| mpp_perm | QTL significance threshold by permutation |
| mpp_proc | MPP QTL analysis |
| mpp_SIM | MPP Simple Interval Mapping |
| MQE_gen_effects | QTL genetic effects multi-QTL effect model |
| MQE_proc | Multi-QTL effect MPP analysis |
| par_clu | Parental clustering |
| parent_cluster.mppData | Parent clustering for 'mppData' objects |
| plot_allele_eff_GE | plot of genome wide QTL allelic effect significance |
| plot.QTLprof | plot QTL profile |
| plot_QTLxEC | plot QTLxEC effect |
| print.summary.mppData | Print summary.mppData object |
| print.summary.QeffRes | Print summary.QeffRes object |
| print.summary.QR2Res | Print summary.QR2Res object |
| QC.mppData | Quality control for 'mppData' objects |
| QTL_effect_GE | MPP GxE QTL genetic effects |
| QTL_effect_main_QxE | Estimation of QTL main effect and QTLxE effect |
| QTL_effect_QxEC | Estimation of QTL effect sensitivity to environmental... |
| QTL_forward | Forward regression QTL model |
| QTL_gen_effects | QTL genetic effects |
| QTL_pred_R2 | Predicted QTL global and partial R squared |
| QTL_R2 | QTL global and partial R squared |
| QTL_R2_GE | MPP GxE QTL R2 |
| QTL_select | QTL candidates selection |
| subset.mppData | Subset 'mppData' object |
| summary.mppData | Summary of 'mppData' object |
| summary.QeffRes | Summary of 'QeffRes' object |
| summary.QR2Res | Summary of 'QR2Res' object |
| USNAM_geno | Reduced genotype data maize US-NAM population |
| USNAM_map | Reduced map maize US-NAM population |
| USNAM_pheno | Reduced phenotype data from Maize US-NAM population |
