estimateLog10LikelihoodTheta: Theta-corrected likelihood computation
In Ahhgust/MMDIT: Mitochondrial mixture project

View source: R/semicontinuousMixtureInterpretation.R

This computes the theta corrected likelihood of a set of alleles hypothesized (unknowns) given a set of observed haplotypes (allelesObserved) as well as a sample of alleles from the relevant population and an estimate of co-ancestry.

estimateLog10LikelihoodTheta(
  allelesObserved,
  allelesThatExplain,
  theta,
  allelesInPopulation,
  populationCounts = NULL
)

`allelesObserved`	vector of alleles observed (knowns) (not database, may be empty)
`allelesThatExplain`	vector of alleles (unknowns haplotypes only)
`theta`	theta-correction (Fst, taken from fst_buckleton)
`allelesInPopulation`	a vector of alleles sampled from the population (also from database, but may in practice come from a different sub-population)
`populationCounts`	a vector of integer weights (parallel to allelesInPopulation)

This estimator is equation 3 in Ge et al. 2010 (doi.org/10.1016/j.legalmed.2010.02.003)

at a high level this computes the likelihood of a set of alleles hypothesized to explain some mixture Some are there by the hypothesis (a victim -> contributing allelesObserved) and others come from a database (unknowns) as well as a sample of alleles from the relevant population (allelesInPopulation)

This estimates the allele frequencies (point estimate from known + unknown + population combined) and weighs the likelihood of the alleles observed based on whether or not the unknowns and the knowns are identical (x-vector). A theta correction is also employed, where theta is an estimate of Fst (fst_buckleton)

It takes in a set of allelesObserved to be in the mixture (according to the hypothesis)

Ahhgust/MMDIT documentation built on Jan. 27, 2021, 11:48 a.m.