net.maizegenetics.taxa.distance

Class DistanceMatrixUtils

net.maizegenetics.taxa.distance.DistanceMatrixUtils

public class DistanceMatrixUtils

Utility functions for distance matrices

Method Detail

getGRMFilenames

public static java.lang.String[] getGRMFilenames(java.lang.String base)

Get Genetic Relationship Matrix (grm) file names.

Parameters:

base - filename base

Returns:

org.jetbrains.dokka.NodeRenderContent@5068a7e1: array of file names. Index 0 is the id filename (.grm.id); Index 1 is the binary matrix (.grm.bin); Index 2 is the binary counts (.grm.N.bin); Index 3 is the raw (text) matrix (.grm.raw); Index 4 is the text matrix (.txt)

getDARwinFilenames

public static java.lang.String[] getDARwinFilenames(java.lang.String base)

Get DARwin file names.

Parameters:

base - filename base

Returns:

org.jetbrains.dokka.NodeRenderContent@7df51b93: array of file names. Index 0 is the id filename (.don); Index 1 is the dissimilarity matrix (.dis)

squaredDistance

public static double squaredDistance(DistanceMatrix mat1,
                                     DistanceMatrix mat2,
                                     boolean weighted)

compute squared distance to second distance matrix. If both matrices have the same size it is assumed that the order of the taxa is identical.

minus

public static DistanceMatrix minus(DistanceMatrix parent,
                                   int taxaToRemove)

Returns a distance matrix with the specified taxa removed.

keepTaxa

public static DistanceMatrix keepTaxa(DistanceMatrix parent,
                                      kotlin.Array[] taxaToKeep)

Parameters:

parent - the DistanceMatrix from which to extract a subset

taxaToKeep - an index of the taxa to keep

Returns:

org.jetbrains.dokka.NodeRenderContent@6aea0781: A DistanceMatrix with all the taxa that are in both parent and taxaToKeep in the same order as taxaToKeep

keepTaxa

public static DistanceMatrix keepTaxa(DistanceMatrix parent,
                                      TaxaList taxaToKeep)

Parameters:

parent - the DistanceMatrix from which to extract a subset

taxaToKeep - a TaxaList of taxa to be kept

Returns:

org.jetbrains.dokka.NodeRenderContent@7c470b47: a DistanceMatrix that contains only the taxa that are in both taxaToKeep and parent. The taxa will be in the same order as taxaToKeep.

clusterBySmallestDistance

public static DistanceMatrix clusterBySmallestDistance(DistanceMatrix orig)

getIBSDistance

public static double getIBSDistance(kotlin.Array[] iMajor,
                                    kotlin.Array[] iMinor,
                                    kotlin.Array[] jMajor,
                                    kotlin.Array[] jMinor)

Calculates the IBS distance between two taxa with bitsets for for major and minor allele

Parameters:

iMajor -

iMinor -

jMajor -

jMinor -

Returns:

org.jetbrains.dokka.NodeRenderContent@6905ec81:

getIBSDistance

public static double getIBSDistance(BitSet iMajor,
                                    BitSet iMinor,
                                    BitSet jMajor,
                                    BitSet jMinor)