net.maizegenetics.analysis.modelfitter

Class GenotypeAdditiveSite

AbstractAdditiveSite

net.maizegenetics.analysis.modelfitter.GenotypeAdditiveSite

All Implemented Interfaces:

AdditiveSite

public class GenotypeAdditiveSite
extends AbstractAdditiveSite

GenotypeAdditiveSite is an AdditiveSite that takes a byte[] array of genotypes as input and converts them to a double[] array. It codes the homozygous major as 2, homozygous minor as 0 and het as 1. It then subtracts the mean value from all elements of the array and sets missing to zero (now the mean). For efficient storage, the values of 0,1,2,3 are stored in a byte array which indexes the double values.

Field Detail

ntaxa

protected int ntaxa

taxaIndex

protected kotlin.Array[] taxaIndex

Constructor Detail

GenotypeAdditiveSite

public GenotypeAdditiveSite(int site,
                            java.lang.String chr,
                            int pos,
                            java.lang.String id,
                            net.maizegenetics.analysis.modelfitter.AdditiveSite.CRITERION selectionCriterion,
                            kotlin.Array[] genotype,
                            byte majorAllele,
                            double majorAlleleFrequency)

Parameters:

site - the site index from the originating GenotypeTable

genotype - genotypeAllTaxa for this site

majorAllele - major allele

majorAlleleFrequency - major allele frequency

Method Detail

reindexTaxa

public void reindexTaxa(kotlin.Array[] taxaIndex,
                        java.util.List<java.lang.Integer> uniqueTaxa)

getCovariate

public kotlin.Array[] getCovariate()

getCovariate

public kotlin.Array[] getCovariate(kotlin.Array[] subset)

getCovariateNoReindex

public kotlin.Array[] getCovariateNoReindex()

getCovariateNoReindex

public kotlin.Array[] getCovariateNoReindex(kotlin.Array[] subset)

getCovariateWithReindex

public kotlin.Array[] getCovariateWithReindex()

getCovariateWithReindex

public kotlin.Array[] getCovariateWithReindex(kotlin.Array[] subset)

serializeAdditiveSites

public static void serializeAdditiveSites(GenotypeTable geno,
                                          java.lang.String outFile)

copy

public AdditiveSite copy()