net.maizegenetics.analysis.association

Class RegRidgeEmmaDoubleMatrix

net.maizegenetics.analysis.association.RegRidgeEmmaDoubleMatrix

public class RegRidgeEmmaDoubleMatrix

Constructor Detail

RegRidgeEmmaDoubleMatrix

public RegRidgeEmmaDoubleMatrix(kotlin.Array[] phenotype,
                                kotlin.Array[] fixedEffects,
                                kotlin.Array[] genotypes,
                                net.maizegenetics.matrixalgebra.Matrix.DoubleMatrixFactory.FactoryType type)

Constructor using native double arrays. Need to specify DoubleMatrix FactoryType

Parameters:

phenotype - ; column matrix of phenotype values. Missing phenotype are coded as NaN. GEBVs are calculate for all lines including missing.

fixedEffects - ; 2D matrix of fixed effects; must not be singular

genotypes - ; matrix of genotypes coded -1, 0, 1. Missing Genotypes as NaN

type - ; Tassel DoubleMatrix Type to use

RegRidgeEmmaDoubleMatrix

public RegRidgeEmmaDoubleMatrix(DoubleMatrix phenotype,
                                DoubleMatrix fixedEffects,
                                DoubleMatrix genotypes)

Constructor using Tassel DoubleMatrix.

Parameters:

phenotype - ; column matrix of phenotype values. Missing phenotype are coded as NaN. GEBVs are calculate for all lines including missing.

fixedEffects - ; 2D matrix of fixed effects; must not be singular

genotypes - ; matrix of genotypes coded -1, 0, 1. Missing Genotypes as NaN

RegRidgeEmmaDoubleMatrix

public RegRidgeEmmaDoubleMatrix(DoubleMatrix phenotype,
                                DoubleMatrix fixedEffects,
                                DoubleMatrix genotypes,
                                DoubleMatrix kinship)

Constructor using Tassel DoubleMatrix. Use when kinship matrix from markers has already been calculated (XXt).

Parameters:

phenotype - ; column matrix of phenotype values. Missing phenotype are coded as NaN. GEBVs are calculate for all lines including missing.

fixedEffects - ; 2D matrix of fixed effects; must not be singular

genotypes - ; matrix of genotypes coded -1, 0, 1. Missing Genotypes as NaN

kinship - ; kinship matrix (XXt) calculated from marker matrix (X)

Method Detail

solve

public void solve()

Solve the mixed model for line GEBVs and marker estimates

getBlups

public kotlin.Array[] getBlups()

Returns:

org.jetbrains.dokka.NodeRenderContent@46c609ae: double array of genomic estimated breeding values (GEBVs) for all lines

getMrkBlups

public kotlin.Array[] getMrkBlups()

Returns:

org.jetbrains.dokka.NodeRenderContent@4df098cd: double array of estimated marker effects for all markers

getGEBVsAsDoubleMatrix

public DoubleMatrix getGEBVsAsDoubleMatrix()

Returns:

org.jetbrains.dokka.NodeRenderContent@3a65c2f8: Tassel DoubleMatrix of genomic estimated breeding values (GEBVs) for all lines

getMrkEstsAsDoubleMatrix

public DoubleMatrix getMrkEstsAsDoubleMatrix()

Returns:

org.jetbrains.dokka.NodeRenderContent@e217be1: Tassel DoubleMatrix of estimated marker effects for all markers