hahmmr (version 1.0.0)

analyze_allele: Analyze allele profile

Description

Analyze allele profile

Usage

analyze_allele(
  bulk,
  t = 1e-05,
  theta_min = 0.08,
  gamma = 20,
  nu = 0.5,
  r = 0.015,
  hmm = "S5",
  fit_theta = FALSE,
  fit_gamma = FALSE,
  theta_start = 0.05,
  verbose = TRUE
)

Value

dataframe Bulk allele profile with CNV states

Arguments

bulk

dataframe Bulk allele profile

t

numeric Transition probability

theta_min

numeric Minimum allele fraction

gamma

numeric Overdispersion parameter

nu

numeric Phase switch rate

r

numeric Alternative allele count bias

hmm

character HMM model to use (S3 or S5)

fit_theta

logical Whether to fit theta_min

fit_gamma

logical Whether to fit gamma

theta_start

numeric Starting value for theta_min

verbose

logical Whether to print progress

Examples

bulk_example = analyze_allele(bulk_example, hmm = 'S5')