Package index • BreedingExperiment

The container

A class that keeps genotypes, phenotypes, pedigree and marker coordinates together, extending RangedSummarizedExperiment.

show(<BreedingExperiment>): Breeding experiment container
BreedingExperiment(): Create a breeding experiment

Relationship matrices

The matrices quantitative genetics runs on, from the pedigree, from the markers, or from both at once.

Amatrix(): Pedigree numerator relationship matrix
Gmatrix(): Genomic relationship matrix
Dmatrix(): Dominance genomic relationship matrix
Hmatrix(): Single-step relationship matrix
inbreeding(): Inbreeding coefficients

Accessors

pedigree() `pedigree<-`(): Pedigree of a breeding experiment
genotypes() `genotypes<-`(): Genotype dosages
genotyped(): Which individuals are genotyped
alleleFrequency(): Allele frequencies and marker summaries

Quality control

filterMarkers(): Filter markers on quality
imputeMarkers(): Impute missing genotypes
sortPedigree(): Order a pedigree so that parents precede their offspring

Data and simulation

demoBreeding: A demonstration breeding population
simulateBreeding(): Simulate a small breeding population

Package

BreedingExperiment-package: BreedingExperiment: breeding data and relationship matrices