Skip to contents

Simulate one clonal evolution and return the CN matrix

simulate_clone.Rd

Runs bridge_sim() until max_cells are alive OR max_time is reached (whichever fires first). If sample_cells is set, a random subsample of that many cells is drawn from the alive population using subsample_sim().

Usage

simulate_clone(
  chromosome,
  allele,
  hotspot_pos,
  params = clonal_params(),
  max_cells = 1000,
  max_time = 300,
  sample_cells = NULL,
  bin_length = 1e+06
)

Arguments

chromosome

Chromosome to simulate (character, e.g. "7").

allele

Allele to track ("A", "B", or "CN").

hotspot_pos

1-based bin index of the position of interest.

params

Parameter list from clonal_params().

max_cells

Stop when this many cells are alive. Default 1000 (effectively no limit when the stopping criterion is time-based).

max_time

Stop at this simulation time. Default 300.

sample_cells

Number of cells to randomly sample from the alive population at the end of the simulation. NULL keeps all alive cells.

bin_length

Bin size in bp. Default 1 Mb.

Value

A list with:

cna_matrix

Integer matrix (cells x bins) for the target allele, after subsampling.

n_alive

Number of cells alive at end of simulation, before sampling.

n_cells

Number of cells in cna_matrix (after sampling).

sim

Full bridge_sim() output (for downstream use).