Trait libprosic::model::priors::PairModel

pub trait PairModel<A: AlleleFreqs, B: AlleleFreqs> {
    fn prior_prob(
        &self, 
        af1: AlleleFreq, 
        af2: AlleleFreq, 
        variant: &Variant
    ) -> LogProb;
    fn joint_prob<L, O>(
        &self, 
        af1: &A, 
        af2: &B, 
        likelihood1: &L, 
        likelihood2: &O, 
        variant: &Variant, 
        n_obs1: usize, 
        n_obs2: usize
    ) -> LogProb
    where
        L: Fn(AlleleFreq, Option<AlleleFreq>) -> LogProb,
        O: Fn(AlleleFreq, Option<AlleleFreq>) -> LogProb;
    fn marginal_prob<L, O>(
        &self, 
        likelihood1: &L, 
        likelihood2: &O, 
        variant: &Variant, 
        n_obs1: usize, 
        n_obs2: usize
    ) -> LogProb
    where
        L: Fn(AlleleFreq, Option<AlleleFreq>) -> LogProb,
        O: Fn(AlleleFreq, Option<AlleleFreq>) -> LogProb;
    fn map<L, O>(
        &self, 
        likelihood1: &L, 
        likelihood2: &O, 
        variant: &Variant, 
        n_obs1: usize, 
        n_obs2: usize
    ) -> (AlleleFreq, AlleleFreq)
    where
        L: Fn(AlleleFreq, Option<AlleleFreq>) -> LogProb,
        O: Fn(AlleleFreq, Option<AlleleFreq>) -> LogProb;
    fn allele_freqs(&self) -> (&A, &B);
}

A prior model for sample pairs.

Required Methods

fn prior_prob(
    &self,
    af1: AlleleFreq,
    af2: AlleleFreq,
    variant: &Variant
) -> LogProb

Calculate prior probability of given combination of allele frequencies.

fn joint_prob<L, O>(
    &self,
    af1: &A,
    af2: &B,
    likelihood1: &L,
    likelihood2: &O,
    variant: &Variant,
    n_obs1: usize,
    n_obs2: usize
) -> LogProb where
    L: Fn(AlleleFreq, Option<AlleleFreq>) -> LogProb,
    O: Fn(AlleleFreq, Option<AlleleFreq>) -> LogProb, 

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

fn marginal_prob<L, O>(
    &self,
    likelihood1: &L,
    likelihood2: &O,
    variant: &Variant,
    n_obs1: usize,
    n_obs2: usize
) -> LogProb where
    L: Fn(AlleleFreq, Option<AlleleFreq>) -> LogProb,
    O: Fn(AlleleFreq, Option<AlleleFreq>) -> LogProb, 

Calculate marginal probability.

fn map<L, O>(
    &self,
    likelihood1: &L,
    likelihood2: &O,
    variant: &Variant,
    n_obs1: usize,
    n_obs2: usize
) -> (AlleleFreq, AlleleFreq) where
    L: Fn(AlleleFreq, Option<AlleleFreq>) -> LogProb,
    O: Fn(AlleleFreq, Option<AlleleFreq>) -> LogProb, 

Calculate maximum a posteriori probability estimate of allele frequencies.

fn allele_freqs(&self) -> (&A, &B)

Return allele frequency spectra.

Implementors

• impl PairModel<ContinuousAlleleFreqs, DiscreteAlleleFreqs> for TumorNormalModel
• impl PairModel<DiscreteAlleleFreqs, ContinuousAlleleFreqs> for SingleCellBulkModel
• impl PairModel<DiscreteAlleleFreqs, DiscreteAlleleFreqs> for FlatNormalNormalModel
• impl PairModel<ContinuousAlleleFreqs, DiscreteAlleleFreqs> for FlatTumorNormalModel