phenoSimulate: PhenoPath simulation

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

PhenoPath simulation

Description

Simulate counts from a pseudotime trajectory using the PhenoPath method.

Usage

phenoSimulate(params = newPhenoParams(), sparsify = TRUE, verbose = TRUE, ...)

Arguments

params	PhenoParams 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 simulate_phenopath that takes a PhenoParams, runs the simulation then converts the output from log-expression to counts and returns a SingleCellExperiment object. The original simulated log-expression values are returned in the LogExprs assay. See simulate_phenopath and the PhenoPath 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).

Paper: 10.1101/159913

Code: https://github.com/kieranrcampbell/phenopath

Examples

if (requireNamespace("phenopath", quietly = TRUE)) {
    sim <- phenoSimulate()
}

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