mfaSimulate: MFA simulation

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

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()
}

Oshlack/splatter documentation built on April 1, 2024, 9:37 a.m.