simulateCells {celda} | R Documentation

## Simulate count data from the celda generative models.

### Description

This function generates a SingleCellExperiment containing a simulated counts matrix in the `"counts"` assay slot, as well as various parameters used in the simulation which can be useful for running celda and are stored in `metadata` slot. The user must provide the desired model (one of celda_C, celda_G, celda_CG) as well as any desired tuning parameters for those model's simulation functions as detailed below.

### Usage

    simulateCells(
      model = c("celda_CG", "celda_C", "celda_G"),
      S = 5,
      CRange = c(50, 100),
      NRange = c(500, 1000),
      C = 100,
      G = 100,
      K = 5,
      L = 10,
      alpha = 1,
      beta = 1,
      gamma = 5,
      delta = 1,
      seed = 12345
    )

### Arguments

`model` | Character. Options available in `celda::availableModels`. Can be one of `"celda_CG"`, `"celda_C"`, or `"celda_G"`. Default `"celda_CG"`.
`S` | Integer. Number of samples to simulate. Default 5. Only used if `model` is one of `"celda_CG"` or `"celda_C"`.
`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). Only used if `model` is one of `"celda_CG"` or `"celda_C"`.
`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).
`C` | Integer. Number of cells to simulate. Default 100. Only used if `model` is `"celda_G"`.
`G` | Integer. The total number of features to be simulated. Default 100.
`K` | Integer. Number of cell populations. Default 5. Only used if `model` is one of `"celda_CG"` or `"celda_C"`.
`L` | Integer. Number of feature modules. Default 10. Only used if `model` is one of `"celda_CG"` or `"celda_G"`.
`alpha` | Numeric. Concentration parameter for Theta. Adds a pseudocount to each cell population in each sample. Default 1. Only used if `model` is one of `"celda_CG"` or `"celda_C"`.
`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. Only used if `model` is one of `"celda_CG"` or `"celda_G"`.
`delta` | Numeric. Concentration parameter for Psi. Adds a pseudocount to each feature in each module. Default 1. Only used if `model` is one of `"celda_CG"` or `"celda_G"`.
`seed` | Integer. Passed to with_seed. For reproducibility, a default value of 12345 is used. If NULL, no calls to with_seed are made.

### Value

A SingleCellExperiment object with simulated count matrix stored in the "counts" assay slot. Function parameter settings are stored in the metadata slot. For `"celda_CG"` and `"celda_C"` models, columns `celda_sample_label` and `celda_cell_cluster` in colData contain simulated sample labels and cell population clusters. For `"celda_CG"` and `"celda_G"` models, column `celda_feature_module` in rowData contains simulated gene modules.

### Examples

    sce <- simulateCells()

[Package celda version 1.8.1 Index]