Multi-Parent Population QTL Analysis

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Documentation for package ‘mppR’ version 1.5.0

• DESCRIPTION file.
• User guides, package vignettes and other documentation.
• Package NEWS.

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