HaplotypeProbabilityOfNormalGivenTumor (picard 2.18.2 API)

java.lang.Object
- picard.fingerprint.HaplotypeProbabilities
- - picard.fingerprint.HaplotypeProbabilityOfNormalGivenTumor

```
public class HaplotypeProbabilityOfNormalGivenTumor
extends HaplotypeProbabilities
```
A wrapper class for any HaplotypeProbabilities instance that will assume that the given evidence is that of a tumor sample and provide an hp for the normal sample that tumor came from. This models possible loss of hetrozygosity where het genotypes turn into a homozygous genotype with probability pLoH.
The shortcoming of this model is that we assume that the events are all independent, but this way they are allowed.

Nested Class Summary
- Nested classes/interfaces inherited from class picard.fingerprint.HaplotypeProbabilities
  HaplotypeProbabilities.Genotype

Constructor Summary

Constructors
Constructor Description

HaplotypeProbabilityOfNormalGivenTumor(HaplotypeProbabilities hpOfTumor, double pLoH)

Constructors
Constructor	Description
`HaplotypeProbabilityOfNormalGivenTumor(HaplotypeProbabilities hpOfTumor, double pLoH)`

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method	Description
`double[]`	`getLikelihoods()`	Returns the likelihoods, in order, of the AA, Aa and aa haplotypes given the evidence
`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.
`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.
`void`	`merge(HaplotypeProbabilities ignored)`	Merges in the likelihood information from the supplied haplotype probabilities object.

Methods inherited from class picard.fingerprint.HaplotypeProbabilities
getHaplotype, getLodMostProbableGenotype, getLogLikelihoods, getMostLikelyGenotype, getMostLikelyHaplotype, getPosteriorProbabilities, getPriorProbablities, scaledEvidenceProbabilityUsingGenotypeFrequencies, shiftedLogEvidenceProbability, shiftedLogEvidenceProbabilityGivenOtherEvidence, shiftedLogEvidenceProbabilityUsingGenotypeFrequencies

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

- Constructor Detail
  - HaplotypeProbabilityOfNormalGivenTumor
```
public HaplotypeProbabilityOfNormalGivenTumor(HaplotypeProbabilities hpOfTumor,
                                              double pLoH)
```
- Method Detail
  - 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
  - getRepresentativeSnp
```
public Snp getRepresentativeSnp()
```
    Description copied from class: HaplotypeProbabilities
    
    Returns a representative SNP for this haplotype. Different subclasses may implement this in different ways, but should do so in a deterministic/repeatable fashion.
    
    Specified by:
    
    getRepresentativeSnp in class HaplotypeProbabilities
  - merge
```
public void merge(HaplotypeProbabilities ignored)
```
    Description copied from class: HaplotypeProbabilities
    
    Merges in the likelihood information from the supplied haplotype probabilities object.
    
    Specified by:
    
    merge in class HaplotypeProbabilities
  - getObsAllele1
```
public int getObsAllele1()
```
    Description copied from class: HaplotypeProbabilities
    
    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.
    
    Overrides:
    
    getObsAllele1 in class HaplotypeProbabilities
    
    Returns:
    
    int
  - getObsAllele2
```
public int getObsAllele2()
```
    Description copied from class: HaplotypeProbabilities
    
    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.
    
    Overrides:
    
    getObsAllele2 in class HaplotypeProbabilities
    
    Returns:
    
    int
  - getTotalObs
```
public int getTotalObs()
```
    Description copied from class: HaplotypeProbabilities
    
    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.
    
    Overrides:
    
    getTotalObs in class HaplotypeProbabilities
    
    Returns:
    
    int
  - hasEvidence
```
public boolean hasEvidence()
```
    Description copied from class: HaplotypeProbabilities
    
    Returns true if evidence has been added, false if the probabilities are just the priors.
    
    Overrides:
    
    hasEvidence in class HaplotypeProbabilities

Class HaplotypeProbabilityOfNormalGivenTumor

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 Detail

HaplotypeProbabilityOfNormalGivenTumor

Method Detail

getLikelihoods

getRepresentativeSnp

merge

getObsAllele1

getObsAllele2

getTotalObs

hasEvidence