picard.fingerprint

Class HaplotypeProbabilityOfNormalGivenTumor

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.

Author:

farjoun

Nested Class Summary

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

HaplotypeProbabilities.Genotype

Constructor Summary

Constructors

Constructor and Description
HaplotypeProbabilityOfNormalGivenTumor(HaplotypeProbabilities hpOfTumor, double pLoH)

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}.
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