get_allele_hmm_s3 function

Make a 3-state allele HMM - allow transitions to netural state

get_allele_hmm_s3(pAD, DP, R, p_s, t, theta_min, 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
• t: numeric Transition probability between haplotype states
• theta_min: numeric Haplotype imbalance
• gamma: numeric Overdispersion in the allele-specific expression
• r: numeric Variant mapping bias

Returns

HMM object