Package index • bridges

All functions

abc_inference(): ABC inference of BFB simulation parameters
bridge_sim(): Gillespie Simulation for Break-Fusion-Bridge (BFB) Processes Modified to support diploid chromosomes (alleles A and B)
clonal_params(): Build a parameter list for clonal simulations
compare_clonal_params(): Compare summary statistics across multiple parameter sets
compute_observed_stats(): Compute summary statistics from a real CNA sample
continue_simulation(): Check if simulation should continue
create_initial_chromosome_sequences(): Create initial chromosome sequences for all alleles
create_tree_annotation(): Create tree annotation for heatmap
derive_hotspot_pos(): Derive hotspot bin position from a CN matrix
detect_bfb(): Detect Breakpoint-Free Branches (BFB) in Phylogenetic Trees
fit(): Main Function for Genomic Distance Calculation and Phylogenetic Tree Construction
get_next_event(): Determine the next event to occur
get_seq_length(): Compute the Length of a Sequence
infer_bin_length(): Infer bin length from a CNA data frame
initialize_simulation(): Helper functions modified for diploid chromosome modeling Initialize simulation state for diploid chromosomes
initialize_with_bfb(): Initialize simulation with BFB events for initial cells (diploid version)
initialize_without_bfb(): Initialize simulation without BFB for initial cells (diploid version)
optimize_tree_ordering(): Optimize tree tip ordering based on distance matrix
plot_abc_results(): Plot ABC posterior distributions
plot_bfb_signature(): Plot BFB-like Signatures Along the Genome
plot_chr_all_heatmap(): Plot Chromosome-wide Heatmap of Copy Number Alterations
plot_clonal_comparison(): Plot summary statistics across clonal simulation conditions
plot_heatmap(): Create comprehensive heatmap with optional phylogenetic tree
prepare_heatmap_matrix(): Prepare matrix data for heatmap plotting
prepare_results(): Prepare final results from simulation
prepare_row_annotations(): Prepare row annotations from a single data frame
process_birth_event(): Process a birth event (diploid version)
process_death_event(): Process a death event
process_tree(): Process tree for heatmap visualization
pseudo_cell_bin_test(): Perform Binomial Test on Pseudo-Cell Delta Values
pseudo_cell_t_test(): Perform T-Test on Pseudo-Cell Delta Values
reconstruct_tree(): Reconstruct Phylogenetic Tree with Copy Number Analysis
run_ABC(): Run a single ABC simulation and compute distance to observed data
run_clonal_replicates(): Run N independent clonal simulations and summarise each
sample_priors(): Sample parameters from prior distributions
sim_bfb_left_and_right_sequences(): Simulate Breakage-Fusion-Bridge (BFB) Cycle for both daughters
simulate_clone(): Simulate one clonal evolution and return the CN matrix
summarise_clone(): Compute summary statistics for a single clonal CN matrix
validate_heatmap_inputs(): Validate input parameters for heatmap plotting