net.maizegenetics.analysis.imputation

Class BiparentalHaplotypeFinder

net.maizegenetics.analysis.imputation.BiparentalHaplotypeFinder

public class BiparentalHaplotypeFinder

Field Detail

myPopulationData

protected PopulationData myPopulationData

initialGenotype

protected GenotypeTable initialGenotype

reportBuilder

protected TableReportBuilder reportBuilder

window

protected int window

The size of the window in which to evaluate haplotypes

overlap

protected int overlap

The extent of overlap between adjacent windows. The overlap is used to assign individual haplotypes to the same parent groups as the previous window.

minNotMissingProportion

protected double minNotMissingProportion

Only cluster haplotypes with a minimum number of non missing values.

minClusterSize

protected int minClusterSize

Only use clusters with minClusterSize taxa as parent haplotypes

maxDifferenceScore

protected int maxDifferenceScore

Haplotypes with a difference score less than or equal to maxDifferenceScore will be assigned to the same cluster. The difference between two non-equal homozygotes is 2, between a homozygote and heterozygote is 1.

minR2

protected double minR2

Filter out sites with less than minR2 average r-square with neighboring sites (window size = 50).

minMaf

protected double minMaf

Filter out sites with minimum allele frequency less than minMaf.

minCoverage

protected double minCoverage

Filter out sites with coverage less than minCoverage.

maxHetDeviation

protected double maxHetDeviation

Filter out sites more than maxHetDeviation * (standard deviation) different from the mean percent heterozygosity.;

Constructor Detail

BiparentalHaplotypeFinder

public BiparentalHaplotypeFinder(PopulationData popdata)

Method Detail

addHaplotypesToReport

public void addHaplotypesToReport(HaplotypeClusterer clusters,
                                  int pos)

getClusterReport

public TableReport getClusterReport()

assignHaplotyes

public void assignHaplotyes()

clusterWindow

public HaplotypeClusterer clusterWindow(GenotypeTable a,
                                        int start,
                                        int length,
                                        int maxdif,
                                        int minNotMissingPerHaplotype)

updatePopulationDataAlleles

public void updatePopulationDataAlleles(java.util.ArrayList<java.util.ArrayList> parentHaplotypes,
                                        java.util.ArrayList<net.maizegenetics.dna.map.Position> positions,
                                        int start,
                                        int length)

mergeMajorHaplotypes

public java.util.ArrayList<net.maizegenetics.analysis.clustering.Haplotype> mergeMajorHaplotypes(HaplotypeClusterer clusterMaker,
                                                                                                 int minClusterSize)

convertGenotypesToParentCalls

public void convertGenotypesToParentCalls()

preFilterSites

public GenotypeTable preFilterSites()

getParentHaplotypesV1

public static java.util.ArrayList<java.util.ArrayList> getParentHaplotypesV1(java.util.ArrayList<java.util.ArrayList> previousParents,
                                                                             java.util.ArrayList<net.maizegenetics.analysis.clustering.Haplotype> candidates,
                                                                             int overlap,
                                                                             boolean forward)

getParentHaplotypes

public static java.util.ArrayList<java.util.ArrayList> getParentHaplotypes(java.util.ArrayList<java.util.ArrayList> previousParents,
                                                                           java.util.ArrayList<net.maizegenetics.analysis.clustering.Haplotype> candidates,
                                                                           int overlap,
                                                                           boolean forward)

doesOverlapMatch

public static boolean doesOverlapMatch(Haplotype h0,
                                       Haplotype h1,
                                       int overlap,
                                       boolean forward)