Simulate concurrent independent linear and cyclic gene processes

Simulate concurrent independent linear and cyclic gene processes

simulate_cylinder(
  N_cells = 5000,
  N_genes = rep(500, 2),
  model = "poisson",
  meanlog = 0,
  sdlog = 0.25,
  scale = 25,
  seed = 1,
  maxT = 15,
  sort = TRUE,
  sparsity = 0.1,
  theta = 10
)

Arguments

N_cells

integer; Number of cells

N_genes

integer vector; Number of genes associated with the linear and cyclic processes

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

sort

boolean; Whether to sort genes based on their peak times

sparsity

numeric; Sparsity of count matrix

theta

numeric; Dipersion parameter for negative binomial model

Value

Returns a gene-by-cell count matrix