Package index • rRACES

Spatial simulation interface

Spatial simulation classes and methods

annotate_forest(): Annotate a plot of cell divisions.

bbox_sampler(): Bounding box sampler

load_samples_forest: Loading samples forests

TissueRectangle$lower_corner: The tissue rectangle lower corner

TissueRectangle$new: Build a new rectangle of tissue.

TissueRectangle$upper_corner: The tissue rectangle upper corner

TissueRectangle: A rectangle in the tissue

SamplesForest$get_coalescent_cells: Retrieving the most recent common ancestors

SamplesForest$get_nodes: Getting forest nodes

SamplesForest$get_samples_info: Retrieving samples' information

SamplesForest$get_species_info: Getting forest species

SamplesForest$get_sticks: Computing the forest sticks

SamplesForest$get_subforest_for: Building subforests

SamplesForest$save: Saving samples forests

SamplesForest: The sample cell ancestor forest

SpatialSimulation$add_mutant: Adding a mutant and its species

SpatialSimulation$border_growth_model: Internal cells duplication

SpatialSimulation$choose_cell_in: Picking one cell in a mutant

SpatialSimulation$death_activation_level: Death activation level

SpatialSimulation$get_added_cells: Getting the cells manually added to the simulation

SpatialSimulation$get_cell: Getting one of the tissue cells

SpatialSimulation$get_cells: Getting the tissue cells

SpatialSimulation$get_clock: Getting the simulated time

SpatialSimulation$get_count_history: Getting the history of the number of cells per species

SpatialSimulation$get_counts: Counting the cell number

SpatialSimulation$get_firing_history: Getting the fired event history

SpatialSimulation$get_firings: Getting the number of fired events

SpatialSimulation$get_lineage_graph: Getting the simulation lineage graph

SpatialSimulation$get_name: Getting the simulation name

SpatialSimulation$get_rates: Getting the species rates

SpatialSimulation$get_rates_update_history: Retrieving the rates update history

SpatialSimulation$get_samples_forest: Getting the samples forest

SpatialSimulation$get_samples_info: Retrieving sample information

SpatialSimulation$get_species: Getting the species

SpatialSimulation$get_tissue_size: Getting the simulated tissue size

SpatialSimulation$history_delta: The delta time between time series samples

SpatialSimulation$mutate_progeny: Generating a mutated progeny

SpatialSimulation$place_cell: Placing one cell in the tissue

SpatialSimulation$run_until: Simulating cell evolution

SpatialSimulation$run_up_to_event: Simulating cell evolution

SpatialSimulation$run_up_to_size: Simulating cell evolution

SpatialSimulation$run_up_to_time: Simulates cell evolution

SpatialSimulation$sample_cells: Sampling a set of cells

SpatialSimulation$schedule_mutation: Scheduling a mutant mutation

SpatialSimulation$search_sample: Searching a rectangular tissue sample

SpatialSimulation$search_samples: Searching rectangular tissue samples

SpatialSimulation$update_rates: Updating species rates

SpatialSimulation$var: Building a simulation status variable

SpatialSimulation: Simulating the cell evolution on a tissue

plot_firings(): Plot the number of stochastic events in the simulation.

plot_muller(): Plot a muller plot

plot_state(): Plot the current state of the simulation.

plot_timeseries(): Plot the current state of the simulation.

plot_tissue(): Plot a tissue

recover_simulation: Loading a simulation

Mutation simulation interface

Mutation simulation classes and methods

Amplification: Creating a CNA amplification

CNA$get_allele: Getting the CNA allele

CNA$get_chromosome: Getting the CNA chromosome

CNA$get_dataframe: Getting the CNA dataframe

CNA$get_length: Getting the CNA length

CNA$get_position_in_chromosome: Getting the CNA chromosome position

CNA$get_src_allele: Getting the CNA source allele

CNA: Creating a CNA

Deletion: Creating a CNA deletion

get_available_tumours_in: Getting the tumour types and studies available for a set-up code.

get_mutation_engine_codes: Getting the supported set-up codes

get_relevant_branches(): Get relevant branch dataframe

load_phylogenetic_forest: Loading a phylogenetic forest

Mutation$get_alt: Getting the mutation altered sequence

Mutation$get_cause: Getting the mutation cause

Mutation$get_chromosome: Getting the mutation chromosome

Mutation$get_dataframe: Getting the mutation dataframe

Mutation$get_position_in_chromosome: Getting the mutation chromosome position

Mutation$get_ref: Getting the mutation reference sequence

Mutation: A single nucleotide variation

MutationEngine$add_exposure: Adding an exposure to the mutation engine

MutationEngine$add_mutant: Adding a mutant specification

MutationEngine$get_SNV_signatures: Getting the SNV signatures

MutationEngine$get_active_germline: Getting the active germline subject

MutationEngine$get_germline_subjects: Getting the germline subjects

MutationEngine$get_indel_signatures: Getting the indel signatures

MutationEngine$get_known_drivers: Getting the known driver mutations

MutationEngine$get_population_descritions: Getting the population descriptions

MutationEngine$infinite_sites_model: Switching on and off the infinite sites model.

MutationEngine$place_mutations: Placing the mutations

MutationEngine$set_germline_subject: Setting the germline subject

MutationEngine: Generating phylogenetic forests

PhylogeneticForest$get_absolute_chromosome_positions: Getting the absolute chromosome positions

PhylogeneticForest$get_bulk_allelic_fragmentation: Getting the bulk allelic fragmentation dataframe

PhylogeneticForest$get_cell_allelic_fragmentation: Getting the cell allelic fragmentation dataframe

PhylogeneticForest$get_coalescent_cells: Retrieving most recent common ancestors

PhylogeneticForest$get_exposures: Getting the timed exposure dataframe

PhylogeneticForest$get_first_occurrences: Getting the mutation first occurrences

PhylogeneticForest$get_germline_mutations: Getting the germinal mutations

PhylogeneticForest$get_germline_subject: Getting the germline subject

PhylogeneticForest$get_nodes: Getting the forest nodes

PhylogeneticForest$get_reference_path: Getting the reference genome path

PhylogeneticForest$get_sampled_cell_CNAs: Getting the sampled cells CNAs

PhylogeneticForest$get_sampled_cell_mutations: Getting the sampled cells mutations

PhylogeneticForest$get_samples_info: Retrieving sample information

PhylogeneticForest$get_species_info: Getting the species

PhylogeneticForest$get_sticks: Computing the forest sticks

PhylogeneticForest$get_subforest_for: Building sub-forests

PhylogeneticForest$save: Saving a phylogenetic forest

PhylogeneticForest$set_reference_path: Setting the reference genome path

PhylogeneticForest: The phylogenetic forest of cells in samples

plot_exposure_timeline(): Plot a signatures exposures

plot_forest(): Plot samples cell division forest.

plot_sticks(): Annotate a plot of cell divisions.

SNV: Creating a SNV

WholeGenomeDoubling: Whole genome doubling events

Sequencing simulation interface

Sequencing simulation methods

BasicIlluminaSequencer$error_rate: Getting error rate

BasicIlluminaSequencer$random_quality_scores: Check non-constant quality score model.

BasicIlluminaSequencer: A basic Illumina sequencer class

ErrorlessIlluminaSequencer: An error-less Illumina sequencer class

label_mutations(): Label mutations using phylogenetic forest data

plot_BAF(): Plot the genome-wide B-Allele Frequency (BAF)

plot_DR(): Plot the genome-wide Depth Ratio (DR)

plot_VAF(): Plot the genome-wide Variant Allele Frequency (VAF)

plot_VAF_histogram(): Plot Histogram of Variant Allele Frequency (VAF)

plot_VAF_marginals(): Plot Marginals of Variant Allele Frequency (VAF)

SampledCell$birth_time: Getting the sampled cell birth time

SampledCell$epistate: Getting the sampled cell epigenetic state

SampledCell$mutant: Getting the sampled cell mutant

SampledCell$mutations: Getting the sampled cell mutations

SampledCell$species: Getting the sampled cell species

SampledCell: A sampled cell

simulate_seq: Simulating the sequencing

simulate_normal_seq: Simulating wild-type sequencing

seq_to_long(): Convert Sequencing Results from Wide to Long Format

Simulation Logics

Simulation Logics

Expression: Represent an expression of value and variable

Formula: First order formulas about simulations

Variable: Represent a simulation quantity