likelihood_allele {hahmmr}

Only compute total log likelihood from an allele HMM

Description

Only compute total log likelihood from an allele HMM

Usage

likelihood_allele(hmm)

Arguments

hmm

HMM object; expect variables x (allele depth), d (total depth), logPi (log transition prob matrix), delta (prior for each state), alpha (alpha for each state), beta (beta for each state), states (states), p_s (phase switch probs)

Value

numeric; total log likelihood

Examples

likelihood_allele(pre_likelihood_hmm)