ZINB-WaVE simulation — zinbSimulate • Splatter

Simulate counts using the ZINB-WaVE method.

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`.

Value

SingleCellExperiment containing simulated counts

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.

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()
}
#> Simulating counts...
#> Creating final dataset...