BASiCSSimulate: BASiCS simulation

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

BASiCS simulation

Description

Simulate counts using the BASiCS method.

Usage

BASiCSSimulate(
  params = newBASiCSParams(),
  sparsify = TRUE,
  verbose = TRUE,
  ...
)

Arguments

params	BASiCSParams 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 BASiCS_Sim that takes a BASiCSParams, runs the simulation then converts the output to a SingleCellExperiment object. See BASiCS_Sim for more details of how the simulation works.

Value

SingleCellExperiment containing simulated counts

References

Vallejos CA, Marioni JC, Richardson S. BASiCS: Bayesian Analysis of Single-Cell Sequencing data. PLoS Computational Biology (2015).

Paper: 10.1371/journal.pcbi.1004333

Code: https://github.com/catavallejos/BASiCS

Examples

if (requireNamespace("BASiCS", quietly = TRUE)) {
    sim <- BASiCSSimulate()
}

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