net.maizegenetics.analysis.distance

Class IBSDistanceMatrix

java.lang.Object

net.maizegenetics.analysis.distance.IBSDistanceMatrix

public class IBSDistanceMatrix
extends Object

This class calculates an identity by state matrix. It is scaled so only non-missing comparison are used. It conducts bit level calculations of IBS for genotypes. Only the two most common alleles are used in the distance calculations.

Please note that when heterozygous genotypes are used, Het to Het distance is 0.5 NOT 0.0. The default along the identity diagonal is 0 (isTrueIBS = false), but changing isTrueIBS = true will calculate the identity.

The distance estimates become wildly inaccurate when too few sites are used to calculate distance. The minSiteComp parameter can be used to control the minimum number of sites used for a calculation. If there are insufficient sites in the estimate, then Double.NaN is returned.

Version:

1.0

Author:

Ed Buckler

Method Summary

Modifier and Type	Method and Description
static double[]	computeHetBitDistances(GenotypeTable theTBA, int taxon1, int taxon2) Compute distance for a pair of taxa.
static double[]	computeHetBitDistances(GenotypeTable theTBA, int taxon1, int taxon2, int minSitesCompared) Compute distance for a pair of taxa.
static double[]	computeHetBitDistances(GenotypeTable theTBA, int taxon1, int taxon2, int minSitesCompared, int firstWord, int lastWord, BitSet maskBadSet) Compute distance for a pair of taxa.
static double[]	computeHetBitDistances(long[] iMj, long[] iMn, long[] jMj, long[] jMn, int minSitesCompared) Calculation of distance using the bit vector of major and minor alleles.
static double[]	computeHetBitDistances(long[] iMj, long[] iMn, long[] jMj, long[] jMn, int minSitesCompared, int firstWord, int lastWord) Calculation of distance using the bit vector of major and minor alleles.
static double[]	computeHetBitDistancesThirdState(long[] iMj, long[] iMn, long[] iMn2, long[] jMj, long[] jMn, long[] jMn2, int minSitesCompared) Calculation of distance using the bit vector of the first three alleles.
static double[]	computeHetBitDistancesThirdState(long[] iMj, long[] iMn, long[] iMn2, long[] jMj, long[] jMn, long[] jMn2, int minSitesCompared, int firstWord, int lastWord) Calculation of distance using the bit vectors of the first three alleles.
static double[]	computeHetDistances(byte[] first, byte[] second, int minSitesComp)
static DistanceMatrix	getInstance(GenotypeTable theAlignment) Compute observed distances for all taxa.
static DistanceMatrix	getInstance(GenotypeTable theAlignment, int minSiteComp, boolean trueIBS, ProgressListener listener, boolean useThirdState) Compute observed distances for all taxa.
static DistanceMatrix	getInstance(GenotypeTable theAlignment, int minSiteComp, ProgressListener listener) Compute observed distances for all taxa.
static DistanceMatrix	getInstance(GenotypeTable theAlignment, ProgressListener listener) Compute observed distances for all taxa.

Methods inherited from class java.lang.Object

equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Method Detail

getInstance

public static DistanceMatrix getInstance(GenotypeTable theAlignment)

Compute observed distances for all taxa. Missing sites are ignored.

Parameters:

theAlignment - Alignment used to computed distances

getInstance

public static DistanceMatrix getInstance(GenotypeTable theAlignment,
                                         ProgressListener listener)

Compute observed distances for all taxa. Missing sites are ignored.

Parameters:

theAlignment - Alignment used to computed distances

listener - Listener to track progress in calculations

getInstance

public static DistanceMatrix getInstance(GenotypeTable theAlignment,
                                         int minSiteComp,
                                         ProgressListener listener)

Compute observed distances for all taxa. Missing sites are ignored.

Parameters:

theAlignment - Alignment used to computed distances

minSiteComp - Minimum number of sites needed to estimate distance

listener - Listener to track progress in calculations

getInstance

public static DistanceMatrix getInstance(GenotypeTable theAlignment,
                                         int minSiteComp,
                                         boolean trueIBS,
                                         ProgressListener listener,
                                         boolean useThirdState)

Compute observed distances for all taxa. Missing sites are ignored.

Parameters:

theAlignment - Alignment used to computed distances

minSiteComp - Minimum number of sites needed to estimate distance

trueIBS - estimate diagonal distance based IBS (default = false, i=i=0.0)

listener - Listener to track progress in calculations

useThirdState -

computeHetDistances

public static double[] computeHetDistances(byte[] first,
                                           byte[] second,
                                           int minSitesComp)

computeHetBitDistances

public static double[] computeHetBitDistances(GenotypeTable theTBA,
                                              int taxon1,
                                              int taxon2)

Compute distance for a pair of taxa.

Parameters:

theTBA - input alignment

taxon1 - index of taxon 1

taxon2 - index of taxon 2

Returns:

array of {distance, number of sites used in comparison}

computeHetBitDistances

public static double[] computeHetBitDistances(GenotypeTable theTBA,
                                              int taxon1,
                                              int taxon2,
                                              int minSitesCompared)

Compute distance for a pair of taxa.

Parameters:

theTBA - input alignment

taxon1 - index of taxon 1

taxon2 - index of taxon 2

minSitesCompared - Minimum number of sites needed to estimate distance

Returns:

array of {distance, number of sites used in comparison}

computeHetBitDistances

public static double[] computeHetBitDistances(GenotypeTable theTBA,
                                              int taxon1,
                                              int taxon2,
                                              int minSitesCompared,
                                              int firstWord,
                                              int lastWord,
                                              BitSet maskBadSet)

Compute distance for a pair of taxa. Optimized for calculations sites within a certain range of underlying word (64 sites chunks) in the TBit array

Parameters:

theTBA - input alignment

taxon1 - index of taxon 1

taxon2 - index of taxon 2

minSitesCompared - Minimum number of sites needed to estimate distance

firstWord - starting word for calculating distance site=(firstWord*64)

lastWord - ending word for calculating distance inclusive site=(lastWord*64+63)

maskBadSet - Optional mask for sites (those set to 1 are kept)

Returns:

array of {distance, number of sites used in comparison}

computeHetBitDistances

public static double[] computeHetBitDistances(long[] iMj,
                                              long[] iMn,
                                              long[] jMj,
                                              long[] jMn,
                                              int minSitesCompared)

Calculation of distance using the bit vector of major and minor alleles.

Parameters:

iMj - Vector of major alleles for taxon i

iMn - Vector of minor alleles for taxon i

jMj - Vector of major alleles for taxon j

jMn - Vector of minor alleles for taxon j

minSitesCompared - Minimum number of sites needed to estimate distance

Returns:

array of {distance, number of sites used in comparison}

computeHetBitDistancesThirdState

public static double[] computeHetBitDistancesThirdState(long[] iMj,
                                                        long[] iMn,
                                                        long[] iMn2,
                                                        long[] jMj,
                                                        long[] jMn,
                                                        long[] jMn2,
                                                        int minSitesCompared)

Calculation of distance using the bit vector of the first three alleles.

Parameters:

iMj - Vector of major alleles for taxon i

iMn - Vector of minor alleles for taxon i

jMj - Vector of major alleles for taxon j

jMn - Vector of minor alleles for taxon j

minSitesCompared - Minimum number of sites needed to estimate distance

Returns:

array of {distance, number of sites used in comparison}

computeHetBitDistances

public static double[] computeHetBitDistances(long[] iMj,
                                              long[] iMn,
                                              long[] jMj,
                                              long[] jMn,
                                              int minSitesCompared,
                                              int firstWord,
                                              int lastWord)

Calculation of distance using the bit vector of major and minor alleles.

Parameters:

iMj - Vector of major alleles for taxon i

iMn - Vector of minor alleles for taxon i

jMj - Vector of major alleles for taxon j

jMn - Vector of minor alleles for taxon j

minSitesCompared - Minimum number of sites needed to estimate distance

firstWord - first world for calculating distance

lastWord - last word for calculating distance inclusive site=(endWord*64+63)

Returns:

array of {distance, number of sites used in comparison}

computeHetBitDistancesThirdState

public static double[] computeHetBitDistancesThirdState(long[] iMj,
                                                        long[] iMn,
                                                        long[] iMn2,
                                                        long[] jMj,
                                                        long[] jMn,
                                                        long[] jMn2,
                                                        int minSitesCompared,
                                                        int firstWord,
                                                        int lastWord)

Calculation of distance using the bit vectors of the first three alleles.

Parameters:

iMj - Vector of major alleles for taxon i

iMn - Vector of minor alleles for taxon i

iMn2 - Vector of second minor alleles for taxon i

jMj - Vector of major alleles for taxon j

jMn - Vector of minor alleles for taxon j

jMn2 - Vector of second minor alleles for taxon j

minSitesCompared - Minimum number of sites needed to estimate distance

firstWord - first world for calculating distance

lastWord - last word for calculating distance inclusive site=(endWord*64+63)

Returns:

array of {distance, number of sites used in comparison}