analyze_joint: Analyze allele and expression profile

In hahmmr: Haplotype-Aware Hidden Markov Model for RNA

Analyze allele and expression profile

Description

Analyze allele and expression profile

Usage

analyze_joint(
  bulk,
  t = 1e-05,
  gamma = 20,
  theta_min = 0.08,
  logphi_min = 0.25,
  hmm = "S15",
  nu = 1,
  min_genes = 10,
  r = 0.015,
  theta_start = 0.05,
  exclude_neu = TRUE,
  fit_gamma = FALSE,
  fit_theta = FALSE,
  verbose = TRUE
)

Arguments

bulk	dataframe Bulk allele and expression profile
t	numeric Transition probability
gamma	numeric Overdispersion parameter
theta_min	numeric Minimum allele fraction
logphi_min	numeric Minimum log2 fold change
hmm	character HMM model to use (S7 or S15)
nu	numeric Phase switch rate
min_genes	integer Minimum number of genes per segment
r	numeric Alternative allele count bias
theta_start	numeric Starting value for theta_min
exclude_neu	logical Whether to exclude neutral segments in retest
fit_gamma	logical Whether to fit gamma
fit_theta	logical Whether to fit theta_min
verbose	logical Whether to print progress

Value

dataframe Bulk allele and expression profile with CNV states

Examples

bulk_example = analyze_joint(bulk_example, hmm = 'S15')

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