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Build a parameter list for clonal simulations

clonal_params.Rd

Returns a complete parameter list with sensible defaults. Any argument can be overridden. Pass the result to run_clonal_replicates() or compare_clonal_params().

Usage

clonal_params(
  bfb_prob = 0.5,
  amp_rate = 0.3,
  del_rate = 0.2,
  positive_selection_rate = 0,
  negative_selection_rate = 0,
  birth_rate = 1,
  death_rate = 0.1,
  lambda = 2,
  rate = 20,
  first_round_of_bfb = TRUE
)

Arguments

bfb_prob

Relative probability of a BFB event per division.

amp_rate

Relative probability of a focal amplification.

del_rate

Relative probability of a focal deletion.

positive_selection_rate

Multiplicative birth-rate boost for cells that have gained a copy at hotspot_pos. 0 = neutral.

negative_selection_rate

Multiplicative death-rate boost for cells that have gained a copy at hotspot_pos. 0 = neutral.

birth_rate

Base cell birth rate.

death_rate

Base cell death rate.

lambda

Mean number of genomic events per daughter cell per division (Poisson).

rate

Scale of focal amp/del events: segment length is drawn from Exp(1/rate).

first_round_of_bfb

If TRUE the founding cell already carries one BFB event, mimicking a clone that initiated from a single BFB.

Value

Named list of simulation parameters.