picard.fingerprint

Class HaplotypeProbabilitiesFromGenotype

java.lang.Object

picard.fingerprint.HaplotypeProbabilities

picard.fingerprint.HaplotypeProbabilitiesFromGenotype

public class HaplotypeProbabilitiesFromGenotype
extends HaplotypeProbabilities

Represents a set of HaplotypeProbabilities that were derived from a single SNP genotype at a point in time.

Nested Class Summary

Nested classes/interfaces inherited from class picard.fingerprint.HaplotypeProbabilities

HaplotypeProbabilities.Genotype

Constructor Summary

Constructors

Constructor and Description
HaplotypeProbabilitiesFromGenotype(Snp snp, HaplotypeBlock haplotypeBlock, double AA, double Aa, double aa)

Method Summary

Modifier and Type	Method and Description
double[]	getLikelihoods() Returns the likelihoods, in order, of the AA, Aa and aa haplotypes given the evidence Mathematically this is P(evidence | haplotype) where haplotype={AA,Aa,aa}.
Snp	getRepresentativeSnp() Returns the SNP who's genotype was used to construct the likelihoods.
void	merge(HaplotypeProbabilities other) Merges in the likelihood information from the supplied haplotype probabilities object.

Methods inherited from class picard.fingerprint.HaplotypeProbabilities

getHaplotype, getLodMostProbableGenotype, getLogLikelihoods, getMostLikelyGenotype, getMostLikelyHaplotype, getObsAllele1, getObsAllele2, getPosteriorProbabilities, getPriorProbablities, getTotalObs, hasEvidence, scaledEvidenceProbabilityUsingGenotypeFrequencies, shiftedLogEvidenceProbability, shiftedLogEvidenceProbabilityGivenOtherEvidence, shiftedLogEvidenceProbabilityUsingGenotypeFrequencies

Methods inherited from class java.lang.Object

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

Constructor Detail

HaplotypeProbabilitiesFromGenotype

public HaplotypeProbabilitiesFromGenotype(Snp snp,
                                          HaplotypeBlock haplotypeBlock,
                                          double AA,
                                          double Aa,
                                          double aa)

Method Detail

getRepresentativeSnp

public Snp getRepresentativeSnp()

Returns the SNP who's genotype was used to construct the likelihoods.

Specified by:

getRepresentativeSnp in class HaplotypeProbabilities

getLikelihoods

public double[] getLikelihoods()

Description copied from class: HaplotypeProbabilities

Returns the likelihoods, in order, of the AA, Aa and aa haplotypes given the evidence Mathematically this is P(evidence | haplotype) where haplotype={AA,Aa,aa}.

Specified by:

getLikelihoods in class HaplotypeProbabilities

merge

public void merge(HaplotypeProbabilities other)

Description copied from class: HaplotypeProbabilities

Merges in the likelihood information from the supplied haplotype probabilities object.

Specified by:

merge in class HaplotypeProbabilities