phenoSimulate {splatter} | R Documentation

## PhenoPath simulation

### Description

Simulate counts from a pseudotime trajectory using the PhenoPath method.

### Usage

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

### Arguments

`params` | PhenoParams 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 `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()
    }

[Package splatter version 1.11.4 Index]