simulateCells.celda_CG: Simulate cells from the celda_CG model

In compbiomed/celda: CEllular Latent Dirichlet Allocation

Description

Generates a simulated counts matrix, cell subpopulation clusters, sample labels, and feature module clusters according to the generative process of the celda_CG model.

Usage

## S3 method for class '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 matrix 'counts', cell population clusters 'z', feature module clusters 'y', sample assignments 'sample.label', and input parameters.

See Also

'celda_C()' for simulating cell subpopulations and 'celda_G()' for simulating feature modules.

Examples

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

compbiomed/celda documentation built on May 25, 2019, 3:58 a.m.