Skip to contents

Detect Breakpoint-Free Branches (BFB) in Phylogenetic Trees

detect_bfb.Rd

This function performs binomial tests across all chromosomes and alleles to detect breakpoint-free branches in a phylogenetic tree reconstruction. It uses pseudo-cell analysis to identify branches where copy number changes occur without breakpoints.

Usage

detect_bfb(fit, threshold = 0.005)

Arguments

fit

A fitted model object containing:

  • all_input_Xs: List of chromosome data with allele information

  • b_dist_func: B distance function

  • g_dist_func: G distance function

  • tree: Phylogenetic tree structure

threshold

Numeric threshold for binomial test probability (default: 0.005)

Value

A data frame containing binomial test results for each chromosome-allele combination:

  • mean: Estimated proportion of successes

  • N_trials: Total number of trials

  • N_successes: Number of successes

  • chr: Chromosome identifier

  • allele: Allele type

  • p.value: P-value from binomial test

  • threshold: Threshold used for testing

Examples

if (FALSE) { # \dontrun{
# Assuming 'fitted_model' is a properly fitted model object
bfb_results <- detect_bfb(fitted_model, threshold = 0.01)
} # }