Run Monte Carlo simulations for one or more patients

Run Monte Carlo simulations for one or more patients

Usage

runSim(
  Lmatrix,
  Rmatrix,
  Cmatrix,
  LRmatrix,
  cells,
  communication_type,
  pats = "all",
  N = 10000,
  itNo = 100,
  av = 20,
  output_folder = NULL,
  file.name = NULL,
  norm = FALSE,
  patient_idx = NULL
)

Arguments

Lmatrix

Cell-by-ligand compatibility matrix.

Rmatrix

Cell-by-receptor compatibility matrix.

Cmatrix

Patient-by-cell-type abundance matrix.

LRmatrix

Ligand-receptor-by-patient tensor.

cells

Character vector of cell-type names.

communication_type

Feature family to simulate ("D", "W", "TT", "CT", or "GSCC").

pats

Number of patients to process, or "all".

N

Number of cells per graph.

itNo

Number of Monte Carlo iterations.

av

Target average degree.

output_folder

Directory used to write the .out files.

file.name

Output filename stem.

norm

Logical; if TRUE, use a uniformized LR baseline.

patient_idx

Optional single patient index to simulate.

Value

Invisibly writes the simulation outputs to disk.