hahmmr (version 1.0.0)

calc_exp_LLR: Calculate LLR for an expression HMM

Description

Calculate LLR for an expression HMM

Usage

calc_exp_LLR(
  Y_obs,
  lambda_ref,
  d,
  phi_mle,
  mu = NULL,
  sig = NULL,
  alpha = NULL,
  beta = NULL
)

Value

numeric Log-likelihood ratio

Arguments

Y_obs

numeric vector Gene expression counts

lambda_ref

numeric vector Reference expression levels

d

numeric vector Total library size

phi_mle

numeric MLE of expression fold change phi (alternative hypothesis)

mu

numeric Mean parameter for the PLN expression model

sig

numeric Dispersion parameter for the PLN expression model

alpha

numeric Hyperparameter for the gamma poisson model (not used)

beta

numeric Hyperparameter for the gamma poisson model (not used)