Package index • ProCESS

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 sample forests

load_sample_forest: Loading sample 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

SampleForest$get_coalescent_cells: Retrieving the most recent common ancestors

SampleForest$get_nodes: Getting forest nodes

SampleForest$get_samples_info: Retrieving the samples' information

SampleForest$get_species_info: Getting forest species

SampleForest$get_sticks: Computing the forest sticks

SampleForest$get_subforest_for: Building sub-forests

SampleForest$save: Saving sample forests

SampleForest: The sample cell ancestor forest

SpatialSimulation: Building a new simulation

TissueSimulation$add_mutant: Adding a mutant and its species

TissueSimulation$border_growth_model: Internal cells duplication

TissueSimulation$choose_cell_in: Picking one cell in a mutant

TissueSimulation$death_activation_level: Death activation level

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

TissueSimulation$get_cell: Getting one of the tissue cells

TissueSimulation$get_cells: Getting the tissue cells

TissueSimulation$get_clock: Getting the simulated time

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

TissueSimulation$get_counts: Counting the cell number

TissueSimulation$get_firing_history: Getting the fired event history

TissueSimulation$get_firings: Getting the number of fired events

TissueSimulation$get_lineage_graph: Getting the simulation lineage graph

TissueSimulation$get_name: Getting the simulation name

TissueSimulation$get_rates: Getting the species rates

TissueSimulation$get_rates_update_history: Retrieving the rates update history

TissueSimulation$get_sample_forest: Getting the sample forest

TissueSimulation$get_samples_forest: Getting the sample forest

TissueSimulation$get_samples_info: Retrieving sample information

TissueSimulation$get_species: Getting the species

TissueSimulation$get_tissue_size: Getting the simulated tissue size

TissueSimulation$history_delta: The delta time between time series samples

TissueSimulation$mutate_progeny: Generating a mutated progeny

TissueSimulation$place_cell: Placing one cell in the tissue

TissueSimulation$run_until: Simulating cell evolution

TissueSimulation$run_up_to_event: Simulating cell evolution

TissueSimulation$run_up_to_size: Simulating cell evolution

TissueSimulation$run_up_to_time: Simulating cell evolution

TissueSimulation$sample_cells: Sampling a set of cells

TissueSimulation$schedule_mutation: Scheduling a mutation

TissueSimulation$search_sample: Searching for a rectangular tissue sample

TissueSimulation$search_samples: Searching rectangular tissue samples

TissueSimulation$update_rates: Updating species rates

TissueSimulation$var: Building a simulation status variable

TissueSimulation: Simulating the cell evolution in a tissue

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

plot_muller(): Draw a Muller plot of the simulation

plot_state(): Plot the current number of cells in a tissue

plot_timeseries(): Plot the number of cells along a 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 data frame

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 available in a setup

get_mutation_engine_codes: Getting the supported setups

get_relevant_branches(): Get the data frame of the relevant branches

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 data frame

Mutation$get_position_in_chromosome: Getting the mutation chromosome position

Mutation$get_ref: Getting the mutation reference sequence

Mutation: Either an SBS or an indel

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_genome_info: Getting the genome information

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_descriptions: Getting the population descriptions

MutationEngine$get_species_rates: Getting the registered species rates

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 data frame

PhylogeneticForest$get_cell_allelic_fragmentation: Getting the cell allelic fragmentation data frame

PhylogeneticForest$get_coalescent_cells: Retrieving the most recent common ancestors

PhylogeneticForest$get_driver_mutations: Getting the driver mutations

PhylogeneticForest$get_exposures: Getting the timed exposure data frame

PhylogeneticForest$get_first_occurrences: Getting the cell in which a mutation emerged

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 the signature exposure timeline of a phylogenetic forest

plot_forest(): Plot a sample forest

plot_sticks(): Annotate a plot of cell divisions

SNV: Creating an SNV

WholeGenomeDoubling: Whole genome doubling events

Sequencing simulation interface

Sequencing simulation methods

BasicIlluminaSequencer$error_rate: Getting the error rate

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

BasicIlluminaSequencer: A basic Illumina sequencer class

ErrorlessIlluminaSequencer: An error-free 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 a Variant Allele Frequency (VAF) histogram

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 of sampled cells

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 simulation state formulas

Variable: Represent a simulation quantity