Run N independent clonal simulations and summarise each — run_clonal

Each replicate is an independent run of simulate_clone(). The simulation stops when max_cells are alive or max_time is reached, then sample_cells cells are drawn using subsample_sim(). Failed simulations (e.g. all cells die) are recorded with NA summary statistics and flagged with failed = TRUE.

Usage

run_clonal_replicates(
  chromosome,
  allele,
  hotspot_pos,
  params = clonal_params(),
  N_replicates = 100,
  max_cells = 1000,
  max_time = 300,
  sample_cells = NULL,
  bin_length = 1e+06,
  n_cores = 1
)

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().
N_replicates: Number of independent clonal evolutions to simulate.
max_cells: Stopping criterion: maximum alive cells.
max_time: Stopping criterion: simulation time limit.
sample_cells: Number of cells to sample after simulation. NULL keeps all.
bin_length: Bin size in bp. Default 1 Mb.
n_cores: Number of parallel cores (uses parallel::mclapply when > 1).

Value

A tibble with one row per replicate and columns for each summary statistic plus replicate, n_alive, and failed.