net.maizegenetics.stats.linearmodels

Class ModelEffectUtils

net.maizegenetics.stats.linearmodels.ModelEffectUtils

public class ModelEffectUtils

Method Detail

getXtY

public static DoubleMatrix getXtY(ModelEffect X,
                                  ModelEffect Y)

getIntegerLevels

public static kotlin.Array[] getIntegerLevels(java.lang.Object[] originalLevels)

getIntegerLevels

public static <T> kotlin.Array[] getIntegerLevels(T[] originalLevels,
                                                  java.util.ArrayList<T> ids)

getIntegerLevelsSortedByGenotype

public static kotlin.Array[] getIntegerLevelsSortedByGenotype(java.lang.String[] originalLevels,
                                                              java.util.ArrayList<java.lang.String> ids)

getIntegerLevels

public static kotlin.Array[] getIntegerLevels(kotlin.Array[] genotypes,
                                              java.util.ArrayList<java.lang.Byte> ids)

Parameters:

genotypes - a byte array of genotypes

ids - an empty array list that will hold the Bytes corresponding to each level

Returns:

org.jetbrains.dokka.NodeRenderContent@38802b96: these genotypes translated into factor levels. On return, ids will hold the Byte labels for each level. Levels will be sorted with homozygotes first then heterozygotes.

genotypesToUnphasedSorted

public static kotlin.Array[] genotypesToUnphasedSorted(kotlin.Array[] genotypes)

getIntegerLevels

public static <T> kotlin.Array[] getIntegerLevels(java.util.ArrayList<T> originalLevels,
                                                  java.util.ArrayList<T> ids)

getIntegerLevels

public static <T> kotlin.Array[] getIntegerLevels(java.util.ArrayList<T> originalLevels)

getIntegerLevels

public static kotlin.Array[] getIntegerLevels(kotlin.Array[] originalLevels)

getNumericCodingForAdditiveModel

public static kotlin.Array[] getNumericCodingForAdditiveModel(java.lang.Object[] marker,
                                                              java.lang.String allele)

getNumericCodingForAdditiveModel

public static kotlin.Array[] getNumericCodingForAdditiveModel(kotlin.Array[] marker,
                                                              byte allele)

Parameters:

marker - the genotypes for a taxon at all sites as bytes

allele - the allele that should be coded as 1. all others will be 0

Returns:

org.jetbrains.dokka.NodeRenderContent@cba40c7: a vector of values (0,1,2) that encode genotypes equal to the dosage of allele