CreateConfigR Documentation

Create the config list for simulation from a Rosette object

Description

Create the config list for simulation from a Rosette object

Usage

CreateConfig(
  object,
  n.sim,
  save.sim,
  type.sim,
  n.rep,
  null.var.group,
  wt.effect,
  n.round,
  n.mut,
  n.pos,
  pop.size,
  mode.sim = "clean",
  mode.rep = "bio",
  seq.shrink = 2,
  seq.depth = 200,
  lib.shrink = 2,
  var.shrink = 0.8,
  pos.flag = TRUE,
  ...
)

Arguments

object

A Rosette object

n.sim

Number of simulations

save.sim

Directory to save the simulation data

type.sim

Type of simulation: growth or binding

n.rep

Number of replicates

null.var.group

Name of the null variant group

wt.effect

Wild-type effect (binding) or doubling rate (growth)

n.round

Number of rounds

n.mut

Number of mutants (currently has to be the same as in the Rosette object) optional, can be inferred from the Rosette object.

n.pos

Number of positions optional, can be inferred from the Rosette object.

pop.size

Cell population size optional, by default 1000 cells per variant.

mode.sim

Simulation mode: "clean" (default) or "reperror"

mode.rep

Replicate mode: "bio" (default) or "tech"

seq.shrink

Shrinkage factor for sequencing dispersion (times seq.disp)

seq.depth

Sequencing depth, by default 200

lib.shrink

Shrinkage factor for library dispersion

var.shrink

Shrinkage factor for variance (var.dist)

pos.flag

whether the simulation is position-centric

...

Other parameters for noise. Reperror: noise.freq, noise.mult

Value

A list of config