simulateCellscelda_C: Simulate cells from the celda_C model

Description Usage Arguments Value See Also Examples

View source: R/celda_C.R

Description

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

Usage

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simulateCellscelda_C(
  model,
  S = 5,
  CRange = c(50, 100),
  NRange = c(500, 1000),
  G = 100,
  K = 5,
  alpha = 1,
  beta = 1,
  seed = 12345,
  ...
)

Arguments

model

Character. Options available in 'celda::availableModels'.

S

Integer. Number of samples to simulate. Default 5.

CRange

Vector of length 2 given the range (min, max) of number of cells for each sample to be randomly generated from the uniform distribution. 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.

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 in each cell population. 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', sample assignments 'sampleLabel', and input parameters.

See Also

'celda_G()' for simulating feature modules and 'celda_CG()' for simulating feature modules and cell populations.

Examples

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celdaCSim <- simulateCells(model = "celda_C", K = 10)
simCounts <- celdaCSim$counts

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