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 |