CV_partition            Cross validation partition
EC_effect               Determine EC effects
IBD.mppData             IBD coding for 'mppData' objects
IBS.mppData             IBS coding for 'mppData' objects
MQE_gen_effects         QTL genetic effects multi-QTL effect model
MQE_proc                Multi-QTL effect MPP analysis
QC.mppData              Quality control for 'mppData' objects
QTL_R2                  QTL global and partial R squared
QTL_R2_GE               MPP GxE QTL R2
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_select              QTL candidates selection
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
create.mppData          Create a multi-parent population data object
design_connectivity     Connected parts of a MPP design
inc_mat_QTL             QTL incidence matrix
mppData                 Complete 'mppData' object
mppData_GE              Example 'mppData' object
mppData_add_pheno       Add new phenotypic values to a 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_SIM               MPP GxE Simple Interval Mapping
mppGE_proc              MPP GxE QTL analysis
mpp_CIM                 MPP Composite Interval Mapping
mpp_CV                  MPP cross-validation
mpp_SIM                 MPP Simple Interval Mapping
mpp_back_elim           Backward elimination on QTL candidates
mpp_forward             MPP QTL analysis using forward regression
mpp_perm                QTL significance threshold by permutation
mpp_proc                MPP QTL analysis
par_clu                 Parental clustering
parent_cluster.mppData
                        Parent clustering for 'mppData' objects
plot.QTLprof            plot QTL profile
plot_QxEC               plot QTLxEC effect
plot_allele_eff_GE      plot of genome wide QTL allelic effect
                        significance
print.summary.QR2Res    Print summary.QR2Res object
print.summary.QeffRes   Print summary.QeffRes object
print.summary.mppData   Print summary.mppData object
subset.mppData          Subset 'mppData' object
summary.QR2Res          Summary of 'QR2Res' object
summary.QeffRes         Summary of 'QeffRes' object
summary.mppData         Summary of 'mppData' object
