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