Struct libprosic::model::priors::tumor_normal_relapse::TumorNormalRelapseModel [−] [src]

pub struct TumorNormalRelapseModel {
    // some fields omitted
}

Methods

impl TumorNormalRelapseModel
[src]

fn new(ploidy: u32, effective_mutation_rate: f64, deletion_factor: f64, insertion_factor: f64, genome_size: u64, heterozygosity: Prob) -> Self

Create new model.

Arguments

  • ploidy - the ploidy in the corresponding normal sample (e.g. 2 for diploid)
  • effective_mutation_rate - the SNV mutation rate per effective cell division in the tumor
  • deletion_factor - ratio of deletions compared to SNV mutation rate
  • insertion_factor - ratio of insertions compared to SNV mutation rate
  • genome_size - the size of the genome
  • heterozygosity - expected heterozygosity in the corresponding normal

Trait Implementations

impl TrioModel<ContinuousAlleleFreqs, ContinuousAlleleFreqs, DiscreteAlleleFreqs> for TumorNormalRelapseModel
[src]

fn prior_prob(&self, af_tumor: AlleleFreq, af_relapse: AlleleFreq, af_normal: AlleleFreq, variant: Variant) -> LogProb

Calculate prior probability of given combination of allele frequencies.

fn joint_prob<L, O, Q>(&self, af_tumor: &ContinuousAlleleFreqs, af_relapse: &ContinuousAlleleFreqs, af_normal: &DiscreteAlleleFreqs, likelihood_tumor: &L, likelihood_relapse: &O, likelihood_normal: &Q, variant: Variant) -> LogProb where L: Fn(AlleleFreq, AlleleFreq) -> LogProb, O: Fn(AlleleFreq, AlleleFreq) -> LogProb, Q: Fn(AlleleFreq, AlleleFreq) -> LogProb

Calculate joint probability of prior with likelihoods for given allele frequency ranges.

fn marginal_prob<L, O, Q>(&self, likelihood_tumor: &L, likelihood_relapse: &O, likelihood_normal: &Q, variant: Variant) -> LogProb where L: Fn(AlleleFreq, AlleleFreq) -> LogProb, O: Fn(AlleleFreq, AlleleFreq) -> LogProb, Q: Fn(AlleleFreq, AlleleFreq) -> LogProb

Calculate marginal probability.

fn map<L, O, Q>(&self, likelihood_tumor: &L, likelihood_relapse: &O, likelihood_normal: &Q, variant: Variant) -> (AlleleFreq, AlleleFreq, AlleleFreq) where L: Fn(AlleleFreq, AlleleFreq) -> LogProb, O: Fn(AlleleFreq, AlleleFreq) -> LogProb, Q: Fn(AlleleFreq, AlleleFreq) -> LogProb

Calculate maximum a posteriori probability estimate of allele frequencies.

fn allele_freqs(&self) -> (&ContinuousAlleleFreqs, &ContinuousAlleleFreqs, &DiscreteAlleleFreqs)

Return allele frequency spectra.