Container and Relationship Matrices for Breeding and Quantitative Genomics

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Documentation for package ‘BreedingExperiment’ version 0.99.4

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

Help Pages

alleleFrequency	Allele frequencies and marker summaries
alleleFrequency-method	Allele frequencies and marker summaries
Amatrix	Pedigree numerator relationship matrix
Amatrix-method	Pedigree numerator relationship matrix
BreedingExperiment	Create a breeding experiment
BreedingExperiment-class	Breeding experiment container
demoBreeding	A demonstration breeding population
Dmatrix	Dominance genomic relationship matrix
Dmatrix-method	Dominance genomic relationship matrix
filterMarkers	Filter markers on quality
filterMarkers-method	Filter markers on quality
genotyped	Which individuals are genotyped
genotyped-method	Which individuals are genotyped
genotypes	Genotype dosages
genotypes-method	Genotype dosages
genotypes<-	Genotype dosages
genotypes<--method	Genotype dosages
Gmatrix	Genomic relationship matrix
Gmatrix-method	Genomic relationship matrix
Hmatrix	Single-step relationship matrix
Hmatrix-method	Single-step relationship matrix
imputeMarkers	Impute missing genotypes
imputeMarkers-method	Impute missing genotypes
inbreeding	Inbreeding coefficients
inbreeding-method	Inbreeding coefficients
pedigree	Pedigree of a breeding experiment
pedigree-method	Pedigree of a breeding experiment
pedigree<-	Pedigree of a breeding experiment
pedigree<--method	Pedigree of a breeding experiment
show-method	Breeding experiment container
simulateBreeding	Simulate a small breeding population
sortPedigree	Order a pedigree so that parents precede their offspring