simpleSimulate: Simple simulation

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

Simple simulation

Description

Simulate counts from a simple negative binomial distribution without simulated library sizes, differential expression etc.

Usage

simpleSimulate(
  params = newSimpleParams(),
  sparsify = TRUE,
  verbose = TRUE,
  ...
)

Arguments

params	SimpleParams 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

Gene means are simulated from a gamma distribution with shape = mean.shape and rate = mean.rate. Counts are then simulated from a negative binomial distribution with mu = means and size = 1 / counts.disp. See SimpleParams for more details of the parameters.

Value

SingleCellExperiment containing simulated counts

Examples

sim <- simpleSimulate()
# Override default parameters
sim <- simpleSimulate(nGenes = 1000, nCells = 50)

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