hahmmr (version 1.0.0)

analyze_joint: 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
)

Value

dataframe Bulk allele and expression profile with CNV states

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

Examples

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