scDDSimulate: scDD simulation

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

scDD simulation

Description

Simulate counts using the scDD method.

Usage

scDDSimulate(
  params = newSCDDParams(),
  plots = FALSE,
  plot.file = NULL,
  sparsify = TRUE,
  verbose = TRUE,
  BPPARAM = SerialParam(),
  ...
)

Arguments

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 BiocParallelParam instance giving the parallel back-end to be used. Default is SerialParam which uses a single core.
...	any additional parameter settings to override what is provided in params.

Details

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.

Value

SingleCellExperiment containing simulated counts

References

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

Examples

sim <- scDDSimulate()

Oshlack/splatter documentation built on Dec. 10, 2024, 3:48 p.m.