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

Description

HaplotypeProbabilitiesFromGenotype(HaplotypeProbabilitiesFromGenotype other)

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

Modifier and Type

Method

Description

HaplotypeProbabilitiesFromGenotype

deepCopy()

double[]

getLikelihoods()

Returns the likelihoods, in order, of the AA, Aa and aa haplotypes given the evidence

Snp

getRepresentativeSnp()

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

HaplotypeProbabilitiesFromGenotype

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, getPosteriorLikelihoods, 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 Details
- HaplotypeProbabilitiesFromGenotype
  
  public HaplotypeProbabilitiesFromGenotype(HaplotypeProbabilitiesFromGenotype other)
- HaplotypeProbabilitiesFromGenotype
  
  public HaplotypeProbabilitiesFromGenotype(Snp snp, HaplotypeBlock haplotypeBlock, double AA, double Aa, double aa)
Method Details
- deepCopy
  
  public HaplotypeProbabilitiesFromGenotype deepCopy()
  
  Specified by:
  
  deepCopy in class HaplotypeProbabilities
- 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}. Will be normalized.
  
  Specified by:
  
  getLikelihoods in class HaplotypeProbabilities
- merge
  
  public HaplotypeProbabilitiesFromGenotype 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

Class HaplotypeProbabilitiesFromGenotype

Nested Class Summary

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

Constructor Summary

Method Summary

Methods inherited from class picard.fingerprint.HaplotypeProbabilities

Methods inherited from class java.lang.Object

Constructor Details

HaplotypeProbabilitiesFromGenotype

HaplotypeProbabilitiesFromGenotype

Method Details

deepCopy

getRepresentativeSnp

getLikelihoods

merge