BASiCS simulation — BASiCSSimulate • Splatter

Simulate counts using the BASiCS method.

Usage

BASiCSSimulate(
  params = newBASiCSParams(),
  sparsify = TRUE,
  verbose = TRUE,
  ...
)

Arguments

params: BASiCSParams 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.

Value

SingleCellExperiment containing simulated counts

Details

This function is just a wrapper around BASiCS_Sim that takes a BASiCSParams, runs the simulation then converts the output to a SingleCellExperiment object. See BASiCS_Sim for more details of how the simulation works.

References

Vallejos CA, Marioni JC, Richardson S. BASiCS: Bayesian Analysis of Single-Cell Sequencing data. PLoS Computational Biology (2015).

Paper: 10.1371/journal.pcbi.1004333

Code: https://github.com/catavallejos/BASiCS

Examples

if (requireNamespace("BASiCS", quietly = TRUE)) {
    sim <- BASiCSSimulate()
}
#> Getting parameters...
#> Warning: Number of gene.params not equal to nGenes, gene.params will be sampled.
#> Warning: Number of cell.params not equal to nCells, cell.params will be sampled.
#> Simulating counts with BASiCS...
#> Creating final dataset...
#> Sparsifying assays...
#> Automatically converting to sparse matrices, threshold = 0.95
#> Skipping 'counts': estimated sparse size 1.08 * dense matrix
#> Done!