get_allele_hmm_s2 function

Make a 2-state allele HMM - no transitions to netural state

get_allele_hmm_s2(pAD, DP, R, p_s, theta, gamma = 20, r = 0.015)

Arguments

• pAD: integer vector Paternal allele counts
• DP: integer vector Total alelle counts
• p_s: numeric vector Phase switch probabilities
• theta: numeric Haplotype imbalance
• gamma: numeric Overdispersion in the allele-specific expression

Returns

HMM object