Reference

All functions

acquire_clone_mutations()

Collect All Mutations for Each Clone in Tree

calc_clone_snv_num()

Calculate Number of SNVs in a Clone

calculate_window_sizes()

Calculate Sizes of Genomic Windows

check_alt_snp_match()

Check Alternative Allele Matches Between SNP List and Simulated Genome

check_genome_chr_length()

Check Chromosome Lengths in Simulated Genome

check_genome_mutations()

Validate Mutations in Simulated Genome

check_loss_segments()

Check Nucleotide Content in Lost Segments

check_ref_snp_match()

Check Reference Genome and SNP List Compatibility

create_cluster_cytoband_anno()

Create Cytoband Annotations for Region Clusters

create_edge_event_table()

Create Edge Event Table from Event Table and Tree

create_event()

Create a Genomic Event Record

create_initial_seg_list()

Create Initial Segment List from Chromosome Arm Table

create_sc_tree_plot()

Create a Cell Lineage Tree Visualization

draw_chr_bar()

Create Chromosome Bar Annotation for ComplexHeatmap

extend_blueprint_cn_for_equal_bin()

Extend Blueprint Copy Number Data for Equal-Sized Bins

find_identical_row_index()

Find Index of an Identical Row in a Data Frame

generate_K2P_matrix()

Generate Kimura 2-Parameter (K2P) Substitution Matrix

generate_blueprint_cn_profiles()

Generate Blueprint Copy Number Profiles

generate_chr_boundary_data()

Generate Chromosome Boundary Data

generate_mock_window_data()

Generate Mock Window Data

get_clone_ancestors()

Get Ancestor Nodes in Phylogenetic Tree

get_edges_between_clones()

Get Edge Names Between Two Nodes in Tree

get_mutations_sc()

Get Mutations for Sampled Single Cells

get_sc_ancestors()

Identify Ancestral Cells in a Lineage

get_segment_info()

Retrieve Genomic Segment Information for a Mutation

group_recurrent_mutations()

Group Recurrent Mutations by Genomic Location

identify_recurrent_mutations()

Identify Recurrent Mutations in Cell Lineage Data

identify_region_clusters()

Identify Clusters of Highly Correlated Genomic Regions

initiate_seg_table()

Initialize Segment Table for Chromosome Regions

insert_mutations()

Insert Mutations into a Genome

insert_snps_to_genome()

Insert SNPs into Reference Genome

introduce_snv()

Introduce Single Nucleotide Variants into a Genome

introduce_snv_sc()

Introduce Single Nucleotide Variants into a Single Cell Genome

merge_fasta_files()

Merge Paternal and Maternal FASTA Files

pick_action_cell()

Select a Clone Type for an Event

pick_transition()

Select a Transition Event Between Clone Types

plot_event_tree()

Plot Event Tree

plot_population_history()

Plot Population Dynamics from Simulation Results

plot_truth_heatmap()

Plot Copy Number Heatmap with Clone Identity Annotations

prepare_tree_data()

Prepare Cell Lineage Data for Tree Visualization

process_cnv_events()

Process and Expand Chromosome-Level CNV Events

process_recurrent_mutation()

Process and Track Recurrent Mutations

sample_action()

Sample a Gillespie Event Type

sample_cells()

Sample Living Cells from Simulation Results

segments_sanity_check()

Perform Sanity Checks on Genomic Segments

select_cell_index()

Select a Specific Cell from a Clone Population

sim_clonal_mutation_nt()

Simulate Nucleotide Changes for Clonal Mutations

sim_clonal_mutation_pos()

Simulate Random Mutation Positions in a Clonal Tree

sim_snv_nt_sc()

Simulate Single Nucleotide Variants for Single Cell Data

simulate_read_dynamic_sc()

Simulate Single-cell Level (dynamics incorporated) Sequencing Reads Using ART in Parallel

simulate_read_sc()

Simulate Clonal-level Single-Cell Sequencing Reads

simulate_sc_dynamic_reads_for_batches()

Simulate Sequencing Reads for Single Cells in Batches

simulate_sc_dynamics()

Simulate Single-Cell Dynamics with Mutations

simulate_single_nt_change()

Simulate Nucleotide Change for a Single Mutation

sub_seg_from_cytoband_anno()

Create Genomic Segments from Cytoband Annotations

subset_interested_profiles()

Subset and Transform Haplotype Copy Number Profiles for Regions of Interest

synth_clone_genome()

Synthesize Clone Genome Based on Events and Mutations

synth_sc_founder_genome()

Synthesize Founder Genome with Structural Variants

synth_sc_genome()

Synthesize Single-Cell Genome

synth_sc_tree_founder_genomes()

Synthesize Founder Genomes for a Cell Lineage Tree

synth_tree_genomes()

Synthesize Genomes for All Clones in Phylogenetic Tree

update_sim_from_event_table()

Update Simulation from Event Table

validate_mutation_check()

Validate Genome Mutation Check Results

vcf_to_snp_list()

Convert Phased VCF Table to SNP Lists by Genotype