simulateCellscelda_CG: Simulate cells from the celda_CG model

Description Usage Arguments Value See Also Examples

View source: R/celda_CG.R

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

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simulateCellscelda_CG(
  model,
  S = 5,
  CRange = c(50, 100),
  NRange = 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::availableModels'.

S

Integer. Number of samples to simulate. Default 5.

CRange

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).

NRange

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 with_seed. For reproducibility, a default value of 12345 is used. If NULL, no calls to with_seed are made.

...

Additional parameters.

Value

List. Contains the simulated matrix 'counts', cell population clusters 'z', feature module clusters 'y', sample assignments 'sampleLabel', and input parameters.

See Also

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

Examples

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celdaCGSim <- simulateCells(model = "celda_CG")

celda documentation built on June 9, 2020, 2 a.m.