scDDSimulate {splatter} | R Documentation |
Simulate counts using the scDD method.
scDDSimulate( params = newSCDDParams(), plots = FALSE, plot.file = NULL, sparsify = TRUE, verbose = TRUE, BPPARAM = SerialParam(), ... )
params |
SCDDParams object containing simulation parameters. |
plots |
logical. whether to generate scDD fold change and validation plots. |
plot.file |
File path to save plots as PDF. |
sparsify |
logical. Whether to automatically convert assays to sparse matrices if there will be a size reduction. |
verbose |
logical. Whether to print progress messages |
BPPARAM |
A |
... |
any additional parameter settings to override what is provided in
|
This function is just a wrapper around simulateSet
that
takes a SCDDParams
, runs the simulation then converts the
output to a SingleCellExperiment
object.
See simulateSet
for more details about how the simulation
works.
SingleCellExperiment containing simulated counts
Korthauer KD, Chu L-F, Newton MA, Li Y, Thomson J, Stewart R, et al. A statistical approach for identifying differential distributions in single-cell RNA-seq experiments. Genome Biology (2016).
Paper: 10.1186/s13059-016-1077-y
Code: https://github.com/kdkorthauer/scDD
## Not run: sim <- scDDSimulate() ## End(Not run)