Run 7-state joint HMM on a pseudobulk profile
run_joint_hmm_s7(
pAD,
DP,
R,
p_s,
Y_obs,
lambda_ref,
d_total,
theta_min = 0.08,
phi_del = 2^(-0.25),
phi_amp = 2^(0.25),
t = 1e-05,
mu = 0,
sig = 1,
gamma = 20,
r = 0.015,
debug = FALSE
)character vector Decoded states
integer vector Paternal allele counts
integer vector Total alelle counts
numeric vector Variant mapping bias direction
numeric vector Phase switch probabilities
numeric vector Observed gene counts
numeric vector Reference expression rates
integer Total library size for expression counts
numeric Minimum haplotype imbalance threshold
numeric Expected fold change for deletion
numeric Expected fold change for amplification
numeric Transition probability between copy number states
numeric Global expression bias
numeric Global expression variance
numeric Overdispersion in the allele-specific expression
numeric Variant mapping bias
logical Whether to print debug messages