analyze_allele: Analyze allele profile

In hahmmr: Haplotype-Aware Hidden Markov Model for RNA

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
)

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

Value

dataframe Bulk allele profile with CNV states

Examples

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

hahmmr documentation built on Oct. 26, 2023, 1:08 a.m.