Package picard.fingerprint

Class 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.

    • 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

      • 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