zinbSimulate: ZINB-WaVE simulation

Description Usage Arguments Details Value References Examples

View source: R/zinb-simulate.R

Description

Simulate counts using the ZINB-WaVE method.

Usage

1
zinbSimulate(params = newZINBParams(), verbose = TRUE, ...)

Arguments

params

ZINBParams object containing simulation parameters.

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

1
sim <- zinbSimulate()

Oshlack/splatter documentation built on June 27, 2018, 10:09 p.m.