zinbSimulate: ZINB-WaVE simulation

In Oshlack/splatter: Simple Simulation of Single-cell RNA Sequencing Data

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()
}

Oshlack/splatter documentation built on Dec. 10, 2024, 3:48 p.m.