zinbSimulate {splatter} | R Documentation

## ZINB-WaVE simulation

### Description

Simulate counts using the ZINB-WaVE method.

### Usage

    zinbSimulate(params = newZINBParams(), sparsify = TRUE, verbose = TRUE, ...)

### Arguments

`params` | ZINBParams object containing simulation parameters.
`sparsify` | logical. Whether to automatically convert assays to sparse matrices if there will be a size reduction.
`verbose` | logical. Whether to print progress messages
`...` | any additional parameter settings to override what is provided in `params`.

### Details

This function is just a wrapper around `zinbSim` that takes a `ZINBParams`, runs the simulation then converts the output to a `SingleCellExperiment` object. See `zinbSim` and the ZINB-WaVE paper for more details about how the simulation works.

### Value

SingleCellExperiment containing simulated counts

### References

Campbell K, Yau C. Uncovering genomic trajectories with heterogeneous genetic and environmental backgrounds across single-cells and populations. bioRxiv (2017).

Risso D, Perraudeau F, Gribkova S, Dudoit S, Vert J-P. ZINB-WaVE: A general and flexible method for signal extraction from single-cell RNA-seq data bioRxiv (2017).

Paper: 10.1101/125112

Code: https://github.com/drisso/zinbwave

### Examples

    if (requireNamespace("zinbwave", quietly = TRUE)) {
        sim <- zinbSimulate()
    }

[Package splatter version 1.14.1 Index]