net.maizegenetics.analysis.modelfitter

Class AddPlusDomModelEffect

net.maizegenetics.analysis.modelfitter.AddPlusDomModelEffect

All Implemented Interfaces:

ModelEffect

public class AddPlusDomModelEffect
implements ModelEffect

A ModelEffect that takes an AdditiveSite as an argument and uses the additiveCovariate from that object to compute a covariate representing dominance. In general, the AdditiveSite will be supplied as the id, although that is not a requirement. The dominance values are calculated as 1 - abs(x - 1) where x is the addivitive value. The values of x are expected to be 0, 1, 2, where 0 and 1 are homozygous genotypes and 1 is the het.

Field Detail

MIN_HETS

public static double MIN_HETS

IMPUTE_DOM

public static boolean IMPUTE_DOM

Constructor Detail

AddPlusDomModelEffect

public AddPlusDomModelEffect(AdditiveSite id,
                             AdditiveSite addSite)

AddPlusDomModelEffect

public AddPlusDomModelEffect(AdditiveSite id,
                             kotlin.Array[] additiveCovariate)

Method Detail

getID

public java.lang.Object getID()

setID

public void setID(java.lang.Object id)

getSize

public int getSize()

getX

public DoubleMatrix getX()

getXtX

public DoubleMatrix getXtX()

getXty

public DoubleMatrix getXty(kotlin.Array[] y)

getyhat

public DoubleMatrix getyhat(DoubleMatrix beta)

getyhat

public DoubleMatrix getyhat(kotlin.Array[] beta)

getLevelCounts

public kotlin.Array[] getLevelCounts()

getNumberOfLevels

public int getNumberOfLevels()

getEffectSize

public int getEffectSize()

getCopy

public ModelEffect getCopy()

getSubSample

public ModelEffect getSubSample(kotlin.Array[] sample)