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.
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).
Examples
if (requireNamespace("mfa", quietly = TRUE)) {
sim <- mfaSimulate()
}
#> Simulating counts...
#> Creating final dataset...
#> Sparsifying assays...
#> Automatically converting to sparse matrices, threshold = 0.95
#> Skipping 'counts': estimated sparse size 1.21 * dense matrix
#> Skipping 'LogExprs': estimated sparse size 1.31 * dense matrix