Package index • tumopp

Run simulation

tumopp() make_args(): Run tumopp

Phylogeny

make_igraph() subtree() subgraph_upstream() trim_root() internal_nodes() distances_from_origin() distances_upstream() sink_cells(): Functions depending on igraph

propagate_drivers(): Functions to deal with driver mutations

Sampling

sample_uniform_regions() sample_random_regions() sample_bulk() sim_sample_single_cell() sim_sample_biopsy() evaluate_mrs() distances_mrs(): Sample cells from a population

dist_genealogy() dist_vaf() pairwise_distances(): Calculate genetic distance from genealogy or VAF

make_vaf() make_longer_vaf() longer_vaf() filter_detectable() sort_vaf(): Utilities for variant allele frequency

make_sample() edge_lengths(): Sprinkle mutations on genealogy

fst() gst() pairwise_fst(): Calculate F_ST from matrix

combn_ids() summarize_capture_rate(): Sample cells from a population

Demography

extract_history() summarize_demography(): Functions for event history

filter_extant() count_extant() filter_common_ancestors(): Functions to modify population data.frame

Summary stats

math_score(): Evaluate heterogeneity

genetic_stats() morphological_stats(): Summarizing functions

stats_dispersion() summary_row() mutate_chisq() rpois_dispersion() tibble_dchisq(): Utilities for dispersion summary_row() and mutate_chisq() calculate various dispersion stats. stats_dispersion() is a shortcut to call them both at once.

Coordinate system

max_abs_xyz() dist_euclidean() transform_rotate(): Utilities for coordinate values

trans_coord_hex(): Transform coordinates into hexagonal grid

add_surface() add_phi(): Extract surface cells with mathematical morphology

as_cuboid() as.data.frame(<cuboid>) as.array(<cuboid>): Binary expression of cell existence

Visualization

augment_genealogy() gggenealogy(): Visualize cell genealogy

plot_capture_rate(): Plot capture_rate ~ nsam of biopsy

plot_tumor3d() snapshot_surface() add_col(): 3D plotting with rgl

histogram_freqspec() plot_lattice2d(): ggplot for frequency spectrum

save_serial_section(): Plot serial sections of 3D tumor

Read and Write

read_confs() read_results() read_tumopp(): Read TSV files in given directories

write_results(): Utilities for writing files

tumopp_path() tumopp_version(): Get information about the tumopp executable