HaplotypeProbabilities (PICARD JDK API Documentation)

java.lang.Object
- picard.fingerprint.HaplotypeProbabilities

Direct Known Subclasses:

HaplotypeProbabilitiesFromGenotype, HaplotypeProbabilitiesFromGenotypeLikelihoods, HaplotypeProbabilitiesFromSequence, HaplotypeProbabilityOfNormalGivenTumor
```
public abstract class HaplotypeProbabilities
extends java.lang.Object
```
Abstract class for storing and calculating various likelihoods and probabilities for haplotype alleles given evidence.

Author:

Tim Fennell

Nested Class Summary

Nested Classes
Modifier and Type	Class and Description
`protected static class`	`HaplotypeProbabilities.Genotype` Log10(P(evidence\| haplotype)) for the 3 different possible haplotypes {aa, ab, bb}

Constructor Summary

Constructors
Modifier Constructor and Description

protected HaplotypeProbabilities(HaplotypeBlock haplotypeBlock)

Constructors
Modifier	Constructor and Description
`protected`	`HaplotypeProbabilities(HaplotypeBlock haplotypeBlock)`

Method Summary

All Methods Instance Methods Abstract Methods Concrete Methods
Modifier and Type	Method and Description
`HaplotypeBlock`	`getHaplotype()` Returns the haplotype for which the probabilities apply.
`abstract 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}.
`double`	`getLodMostProbableGenotype()` Returns the LOD score between the most probable haplotype and the second most probable.
`double[]`	`getLogLikelihoods()`
`DiploidGenotype`	`getMostLikelyGenotype(Snp snp)` Gets the genotype for this Snp given the most likely haplotype.
`DiploidHaplotype`	`getMostLikelyHaplotype()` Gets the most likely haplotype given the probabilities.
`int`	`getObsAllele1()` Returns the number of observations of alleles supporting the first/major haplotype allele.
`int`	`getObsAllele2()` Returns the number of observations of alleles supporting the second/minor haplotype allele.
`double[]`	`getPosteriorProbabilities()` Returns the posterior probabilities using the population frequency as a prior.
`double[]`	`getPriorProbablities()`
`abstract Snp`	`getRepresentativeSnp()` Returns a representative SNP for this haplotype.
`int`	`getTotalObs()` Returns the total number of observations of any allele.
`boolean`	`hasEvidence()` Returns true if evidence has been added, false if the probabilities are just the priors.
`abstract void`	`merge(HaplotypeProbabilities other)` Merges in the likelihood information from the supplied haplotype probabilities object.
`double`	`scaledEvidenceProbabilityUsingGenotypeFrequencies(double[] genotypeFrequencies)` This function returns the scaled probability of the evidence collected given a vector of priors on the haplotype using the internal likelihood, which may be scaled by an unknown factor.
`double`	`shiftedLogEvidenceProbability()` Returns log (p(evidence)) + c assuming that the prior on haplotypes is given by the internal haplotypeFrequencies
`double`	`shiftedLogEvidenceProbabilityGivenOtherEvidence(HaplotypeProbabilities otherHp)` returns the log-probability the evidence, using as priors the posteriors of another object
`double`	`shiftedLogEvidenceProbabilityUsingGenotypeFrequencies(double[] genotypeFrequencies)`

Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

- Constructor Detail
  - HaplotypeProbabilities
```
protected HaplotypeProbabilities(HaplotypeBlock haplotypeBlock)
```
- Method Detail
  - getHaplotype
```
public HaplotypeBlock getHaplotype()
```
    Returns the haplotype for which the probabilities apply.
  - getPriorProbablities
```
public double[] getPriorProbablities()
```
  - getPosteriorProbabilities
```
public double[] getPosteriorProbabilities()
```
    Returns the posterior probabilities using the population frequency as a prior.
  - getLikelihoods
```
public abstract 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}.
  - getLogLikelihoods
```
public double[] getLogLikelihoods()
```
  - getRepresentativeSnp
```
public abstract Snp getRepresentativeSnp()
```
    Returns a representative SNP for this haplotype. Different subclasses may implement this in different ways, but should do so in a deterministic/repeatable fashion.
  - getObsAllele1
```
public int getObsAllele1()
```
    Returns the number of observations of alleles supporting the first/major haplotype allele. Strictly this doesn't make sense for all subclasses, but it's nice to have it part of the API so a default implementation is provided here.
    
    Returns:
    
    int
  - getObsAllele2
```
public int getObsAllele2()
```
    Returns the number of observations of alleles supporting the second/minor haplotype allele. Strictly this doesn't make sense for all subclasses, but it's nice to have it part of the API so a default implementation is provided here.
    
    Returns:
    
    int
  - getTotalObs
```
public int getTotalObs()
```
    Returns the total number of observations of any allele. Strictly this doesn't make sense for all subclasses, but it's nice to have it part of the API so a default implementation is provided here.
    
    Returns:
    
    int
  - hasEvidence
```
public boolean hasEvidence()
```
    Returns true if evidence has been added, false if the probabilities are just the priors.
  - merge
```
public abstract void merge(HaplotypeProbabilities other)
```
    Merges in the likelihood information from the supplied haplotype probabilities object.
  - getMostLikelyHaplotype
```
public DiploidHaplotype getMostLikelyHaplotype()
```
    Gets the most likely haplotype given the probabilities.
  - getMostLikelyGenotype
```
public DiploidGenotype getMostLikelyGenotype(Snp snp)
```
    Gets the genotype for this Snp given the most likely haplotype.
  - scaledEvidenceProbabilityUsingGenotypeFrequencies
```
public double scaledEvidenceProbabilityUsingGenotypeFrequencies(double[] genotypeFrequencies)
```
    This function returns the scaled probability of the evidence collected given a vector of priors on the haplotype using the internal likelihood, which may be scaled by an unknown factor. This factor causes the result to be scaled, hence the name. Mathematically: P(Evidence| P(h_i)=F_i) = \sum_i P(Evidence | h_i) P(h_i) = \sum_i P(Evidence | h_i) F_i = c * \sum_i Likelihood_i * F_i Here, h_i are the three possible haplotypes, F_i are the given priors, and Likelihood_i are the stored likelihoods which are scaled from the actually likelihoods by an unknown factor, c. Note that the calculation ignores the internal haplotype probabilities (i.e. priors)
    
    Parameters:
    
    genotypeFrequencies - vector of (possibly scaled) probabilities of the three haplotypes
    
    Returns:
    
    P(evidence | P_h)) / c
  - shiftedLogEvidenceProbabilityUsingGenotypeFrequencies
```
public double shiftedLogEvidenceProbabilityUsingGenotypeFrequencies(double[] genotypeFrequencies)
```
  - shiftedLogEvidenceProbabilityGivenOtherEvidence
```
public double shiftedLogEvidenceProbabilityGivenOtherEvidence(HaplotypeProbabilities otherHp)
```
    returns the log-probability the evidence, using as priors the posteriors of another object
    
    Parameters:
    
    otherHp - an additional HaplotypeProbabilities object representing the same underlying HaplotypeBlock
    
    Returns:
    
    log10( P(evidence| P(h_i)=P(h_i|otherHp) ) + c where c is an unknown constant
  - shiftedLogEvidenceProbability
```
public double shiftedLogEvidenceProbability()
```
    Returns log (p(evidence)) + c assuming that the prior on haplotypes is given by the internal haplotypeFrequencies
  - getLodMostProbableGenotype
```
public double getLodMostProbableGenotype()
```
    Returns the LOD score between the most probable haplotype and the second most probable.

Class HaplotypeProbabilities

Nested Class Summary

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Constructor Detail

HaplotypeProbabilities

Method Detail

getHaplotype

getPriorProbablities

getPosteriorProbabilities

getLikelihoods

getLogLikelihoods

getRepresentativeSnp

getObsAllele1

getObsAllele2

getTotalObs

hasEvidence

merge

getMostLikelyHaplotype

getMostLikelyGenotype

scaledEvidenceProbabilityUsingGenotypeFrequencies

shiftedLogEvidenceProbabilityUsingGenotypeFrequencies

shiftedLogEvidenceProbabilityGivenOtherEvidence

shiftedLogEvidenceProbability

getLodMostProbableGenotype