simpleSimulate: Simple simulation

Description Usage Arguments Details Value Examples

View source: R/simple-simulate.R

Description

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

Usage

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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

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

splatter documentation built on Dec. 3, 2020, 2:01 a.m.