viterbi_joint function

Viterbi algorithm for joint HMM, can only handle one set of observations

viterbi_joint(hmm)

Arguments

• hmm: HMM object; expect variables x (allele depth), d (total depth), y (expression count), l (cell total library size), lambda (reference expression rate), mu (global expression mean), sig (global expression standard deviation), logPi (log transition prob matrix), phi (expression fold change for each state), delta (prior for each state), alpha (alpha for each state), beta (beta for each state), states (states), p_s (phase switch probs)

Returns

character vector Decoded states