calc_exp_LLR: Calculate LLR for an expression HMM

In whtns/numbat: Haplotype-Aware CNV Analysis from scRNA-Seq

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
)

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)

Value

numeric Log-likelihood ratio

whtns/numbat documentation built on Nov. 8, 2022, 10:48 a.m.