net.maizegenetics.analysis.association

Class CompressedDoubleMatrix

net.maizegenetics.analysis.association.CompressedDoubleMatrix

public class CompressedDoubleMatrix

Field Detail

kinshipMatrix

protected DistanceMatrix kinshipMatrix

theClusters

protected TreeClusters theClusters

numberOfGroups

protected int numberOfGroups

adjustmentMatrix

protected DoubleMatrix adjustmentMatrix

compressedMatrix

protected DoubleMatrix compressedMatrix

distance2clusterIndex

protected kotlin.Array[] distance2clusterIndex

groupMembers

protected kotlin.Array[] groupMembers

Constructor Detail

CompressedDoubleMatrix

public CompressedDoubleMatrix(DistanceMatrix kinship,
                              Tree theTree)

Method Detail

init

protected void init()

getNumberOfGroups

public int getNumberOfGroups()

setNumberOfGroups

public void setNumberOfGroups(int numberOfGroups)

This sets the number of groups and calculates the output matrices. It must be run to set the number of groups before retrieving the compressed and adjustment matrices.

Parameters:

numberOfGroups - the number of groups into which the taxa should be compressed

getCompressedMatrix

public DoubleMatrix getCompressedMatrix(net.maizegenetics.analysis.association.CompressedDoubleMatrix.kinshipMethod km)

Parameters:

km - the kinship method used to calculate the group kinships

Returns:

org.jetbrains.dokka.NodeRenderContent@27d296e6: the compressed distance matrix for the set number of groups

getAdjustmentMatrix

public DoubleMatrix getAdjustmentMatrix()

Returns:

org.jetbrains.dokka.NodeRenderContent@24046d26: the matrix used to post-multiply the Z matrix to produce the compressed Z matrix

getCompressedZKZ

public DoubleMatrix getCompressedZKZ(DoubleMatrix Z,
                                     net.maizegenetics.analysis.association.CompressedDoubleMatrix.kinshipMethod km)

getCompressedZ

public DoubleMatrix getCompressedZ(DoubleMatrix originalZ)