mfaSimulate {splatter} | R Documentation

## MFA simulation

### Description

Simulate a bifurcating pseudotime path using the mfa method.

### Usage

    mfaSimulate(params = newMFAParams(), sparsify = TRUE, verbose = TRUE, ...)

### Arguments

`params` | MFAParams 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 `create_synthetic` that takes a `MFAParams`, runs the simulation then converts the output from log-expression to counts and returns a `SingleCellExperiment` object. See `create_synthetic` and the mfa paper for more details about how the simulation works.

### Value

SingleCellExperiment containing simulated counts

### References

Campbell KR, Yau C. Probabilistic modeling of bifurcations in single-cell gene expression data using a Bayesian mixture of factor analyzers. Wellcome Open Research (2017).

Paper: 10.12688/wellcomeopenres.11087.1

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

### Examples

    if (requireNamespace("mfa", quietly = TRUE)) {
        sim <- mfaSimulate()
    }

[Package splatter version 1.18.2 Index]