# Multi-Parent Population QTL Analysis

## Documentation for package ‘mppR’ version 1.5.0

- DESCRIPTION file
- User guides, package vignettes and other documentation
- Package NEWS
- Package README

## Help Pages

create.mppData | Create a multi-parent population data object
CV_partition | Cross validation partition
design_connectivity | Connected parts of a MPP design
EC_effect | Determine EC effects
IBD.mppData | IBD coding for 'mppData' objects
IBS.mppData | IBS coding for 'mppData' objects
inc_mat_QTL | QTL incidence matrix
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
mppGE_CIM | MPP GxE Composite Interval Mapping
mppGE_proc | MPP GxE QTL analysis
mppGE_SIM | MPP GxE Simple Interval Mapping
mpp_back_elim | Backward elimination on QTL candidates
mpp_CIM | MPP Composite Interval Mapping
mpp_CV | MPP cross-validation
mpp_forward | MPP QTL analysis using forward regression
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
parent_cluster.mppData | Parent clustering for 'mppData' objects
par_clu | Parental clustering
plot.QTLprof | plot QTL profile
plot_allele_eff_GE | plot of genome wide QTL allelic effect significance
plot_QxEC | 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_QEI | Main and QTL by environment interaction model
QTL_effect_main_QxEC | Estimation of a model with main and QTL by environmental sensitivity terms
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