net.maizegenetics.analysis.imputation

Class PopulationData

net.maizegenetics.analysis.imputation.PopulationData

public class PopulationData

Field Detail

name

public java.lang.String name

chromosome

public java.lang.String chromosome

members

public java.util.ArrayList<java.lang.String> members

snpIndex

public BitSet snpIndex

parent1

public java.lang.String parent1

parent2

public java.lang.String parent2

contribution1

public double contribution1

contribution2

public double contribution2

Fgen

public int Fgen

inbredCoef

public double inbredCoef

original

public GenotypeTable original

imputed

public GenotypeTable imputed

alleleA

public kotlin.Array[] alleleA

alleleC

public kotlin.Array[] alleleC

useSubpopulations

public boolean useSubpopulations

Method Detail

readPedigreeFile

public static java.util.ArrayList<net.maizegenetics.analysis.imputation.PopulationData> readPedigreeFile(java.lang.String popFilename)

Parameters:

popFilename - the name of the file containing pedigree information for a group of populations

Returns:

org.jetbrains.dokka.NodeRenderContent@5e64d3cd: a HashMap of family names (keys) and associated PopulationData objects (values) containing information for the families in the pedigree file

readPedigreeFile

public static java.util.ArrayList<net.maizegenetics.analysis.imputation.PopulationData> readPedigreeFile(java.lang.String popFilename,
                                                                                                         java.lang.String chrname,
                                                                                                         boolean includeParents)

Parameters:

popFilename - the name of the file containing pedigree information for a group of populations

includeParents - should the parents be included as family members?

Returns:

org.jetbrains.dokka.NodeRenderContent@623654f3: a HashMap of family names (keys) and associated PopulationData objects (values) containing information for the families in the pedigree file