Package picard.fingerprint
Class HaplotypeProbabilitiesFromGenotype
java.lang.Object
picard.fingerprint.HaplotypeProbabilities
picard.fingerprint.HaplotypeProbabilitiesFromGenotype
Represents a set of HaplotypeProbabilities that were derived from a single SNP
genotype at a point in time.
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Nested Class Summary
Nested classes/interfaces inherited from class picard.fingerprint.HaplotypeProbabilities
HaplotypeProbabilities.Genotype
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Constructor Summary
ConstructorsConstructorDescriptionHaplotypeProbabilitiesFromGenotype
(Snp snp, HaplotypeBlock haplotypeBlock, double AA, double Aa, double aa) -
Method Summary
Modifier and TypeMethodDescriptiondeepCopy()
double[]
Returns the likelihoods, in order, of the AA, Aa and aa haplotypes given the evidenceReturns the SNP who's genotype was used to construct the likelihoods.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
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Constructor Details
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HaplotypeProbabilitiesFromGenotype
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HaplotypeProbabilitiesFromGenotype
public HaplotypeProbabilitiesFromGenotype(Snp snp, HaplotypeBlock haplotypeBlock, double AA, double Aa, double aa)
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Method Details
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deepCopy
- Specified by:
deepCopy
in classHaplotypeProbabilities
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getRepresentativeSnp
Returns the SNP who's genotype was used to construct the likelihoods.- Specified by:
getRepresentativeSnp
in classHaplotypeProbabilities
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getLikelihoods
public double[] getLikelihoods()Description copied from class:HaplotypeProbabilities
Returns the likelihoods, in order, of the AA, Aa and aa haplotypes given the evidenceMathematically this is P(evidence | haplotype) where haplotype={AA,Aa,aa}. Will be normalized.
- Specified by:
getLikelihoods
in classHaplotypeProbabilities
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merge
Description copied from class:HaplotypeProbabilities
Merges in the likelihood information from the supplied haplotype probabilities object.- Specified by:
merge
in classHaplotypeProbabilities
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