Simulate cells from the cell/feature bi-clustering generative model

This function generates a list containing a simulated counts matrix, as well as various parameters used in the simulation which can be useful for running celda.

# S3 method for celda_CG
simulateCells(model, S = 5, C.Range = c(50, 100),
  N.Range = c(500, 1000), G = 100, K = 5, L = 10, alpha = 1,
  beta = 1, gamma = 5, delta = 1, seed = 12345, ...)

Arguments

model	Character. Options available in `celda::available.models`.
S	Integer. Number of samples to simulate. Default 5.
C.Range	Integer vector. A vector of length 2 that specifies the lower and upper bounds of the number of cells to be generated in each sample. Default c(50, 100).
N.Range	Integer vector. A vector of length 2 that specifies the lower and upper bounds of the number of counts generated for each cell. Default c(500, 1000).
G	Integer. The total number of features to be simulated. Default 100.
K	Integer. Number of cell populations. Default 5.
L	Integer. Number of feature modules. Default 10.
alpha	Numeric. Concentration parameter for Theta. Adds a pseudocount to each cell population in each sample. Default 1.
beta	Numeric. Concentration parameter for Phi. Adds a pseudocount to each feature module in each cell population. Default 1.
gamma	Numeric. Concentration parameter for Eta. Adds a pseudocount to the number of features in each module. Default 5.
delta	Numeric. Concentration parameter for Psi. Adds a pseudocount to each feature in each module. Default 1.
seed	Integer. Passed to set.seed(). Default 12345.
...	Additional parameters.

Value

List. Contains the simulated counts matrix, derived cell cluster assignments, the provided parameters, and estimated Dirichlet distribution parameters for the model.

Examples

celda.sim = simulateCells(model="celda_CG")