public class HaplotypeProbabilitiesFromGenotype extends HaplotypeProbabilities
HaplotypeProbabilities.Genotype
Constructor and Description |
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HaplotypeProbabilitiesFromGenotype(Snp snp,
HaplotypeBlock haplotypeBlock,
double AA,
double Aa,
double aa) |
Modifier and Type | Method and Description |
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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}.
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Snp |
getRepresentativeSnp()
Returns the SNP who's genotype was used to construct the likelihoods.
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void |
merge(HaplotypeProbabilities other)
Merges in the likelihood information from the supplied haplotype probabilities object.
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getHaplotype, getLodMostProbableGenotype, getLogLikelihoods, getMostLikelyGenotype, getMostLikelyHaplotype, getObsAllele1, getObsAllele2, getPosteriorProbabilities, getPriorProbablities, getTotalObs, hasEvidence, scaledEvidenceProbabilityUsingGenotypeFrequencies, shiftedLogEvidenceProbability, shiftedLogEvidenceProbabilityGivenOtherEvidence, shiftedLogEvidenceProbabilityUsingGenotypeFrequencies
public HaplotypeProbabilitiesFromGenotype(Snp snp, HaplotypeBlock haplotypeBlock, double AA, double Aa, double aa)
public Snp getRepresentativeSnp()
getRepresentativeSnp
in class HaplotypeProbabilities
public double[] getLikelihoods()
HaplotypeProbabilities
getLikelihoods
in class HaplotypeProbabilities
public void merge(HaplotypeProbabilities other)
HaplotypeProbabilities
merge
in class HaplotypeProbabilities