Simulate a multi-level lineage differentiation process coupled with cell cycle

Simulate a multi-level lineage differentiation process coupled with cell cycle

simulate_coral(
  N_cells = 15 * rep(100, 7),
  N_genes = 2 * rep(100, 7),
  N_genes_CC = 400,
  model = "poisson",
  meanlog = 0,
  sdlog = 0.25,
  scale = 25,
  scale_l = 2,
  seed = 1,
  maxT = 10,
  maxT_CC = 20,
  sparsity = NULL,
  theta = 10
)

Arguments

N_cells

integer vector; Number of cells associated with the differentiation process

N_genes

integer vector; Number of genes associated with the cell cycle process

model

character; Count model ("poisson" or "negbin")

meanlog

numeric; Mean of log normal distribution

sdlog

numeric; Standard deviation of log normal distribution

scale

numeric; Scale of UMI counts

seed

integer; Random seed

maxT

numeric; Maximum cell pseudotime of each lineage in the differentiation process

maxT_CC

numeric; Maximum cell pseudotime of the cell cycle process

sparsity

numeric; Sparsity of count matrix

theta

numeric; Dipersion parameter for negative binomial model

Value

Returns a gene-by-cell count matrix