net.maizegenetics.analysis.imputation

Class ImputeCrossProgeny

java.lang.Object

net.maizegenetics.analysis.imputation.ImputeCrossProgeny

public class ImputeCrossProgeny
extends Object

Constructor Summary

Constructors

Constructor and Description
ImputeCrossProgeny()

Method Summary

Modifier and Type	Method and Description
void	fillgaps(byte[] states)
void	improveImputedProgenyStates()
void	imputeAll()
byte[]	imputeCrossFromParents(String progeny, byte[][] hap0, byte[][] hap1)
byte[]	imputeCrossFromParentsUsingProbabilities(String progeny, double[][] hapProb0, double[][] hapProb1, double[][] probObsGivenState)
void	setHaplotypeMap(String parentHaplotypeFilename)
void	setImputedGenotypeOutFilename(String imputedGenotypeOutFilename)
void	setMyGenotype(GenotypeTable myGenotype)
void	setParentage(String parentageFilename)
void	setParentCallInputFilename(String parentCallFilename)
void	setParentcallOutFilename(String parentcallOutFilename)
void	setPhasedParentOutFilename(String phasedParentOutFilename)
void	setPlotList(List<String[]> plotList)
void	updateStateObsCounts(long[][] counts, byte[][] hap0, byte[][] hap1, byte[] states, String progenyName)

Methods inherited from class java.lang.Object

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

Constructor Detail

ImputeCrossProgeny

public ImputeCrossProgeny()

Method Detail

setPlotList

public void setPlotList(List<String[]> plotList)

imputeAll

public void imputeAll()

imputeCrossFromParents

public byte[] imputeCrossFromParents(String progeny,
                                     byte[][] hap0,
                                     byte[][] hap1)

improveImputedProgenyStates

public void improveImputedProgenyStates()

imputeCrossFromParentsUsingProbabilities

public byte[] imputeCrossFromParentsUsingProbabilities(String progeny,
                                                       double[][] hapProb0,
                                                       double[][] hapProb1,
                                                       double[][] probObsGivenState)

updateStateObsCounts

public void updateStateObsCounts(long[][] counts,
                                 byte[][] hap0,
                                 byte[][] hap1,
                                 byte[] states,
                                 String progenyName)

fillgaps

public void fillgaps(byte[] states)

setParentCallInputFilename

public void setParentCallInputFilename(String parentCallFilename)

setMyGenotype

public void setMyGenotype(GenotypeTable myGenotype)

setParentage

public void setParentage(String parentageFilename)

setHaplotypeMap

public void setHaplotypeMap(String parentHaplotypeFilename)

setImputedGenotypeOutFilename

public void setImputedGenotypeOutFilename(String imputedGenotypeOutFilename)

setParentcallOutFilename

public void setParentcallOutFilename(String parentcallOutFilename)

setPhasedParentOutFilename

public void setPhasedParentOutFilename(String phasedParentOutFilename)