mfaSimulate: MFA simulation

Description Usage Arguments Details Value References Examples

View source: R/mfa-simulate.R

Description

Simulate a bifurcating pseudotime path using the mfa method.

Usage

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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

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

splatter documentation built on Dec. 3, 2020, 2:01 a.m.