splatPopSimulateSample: splatPopSimulateSample simulation

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

splatPopSimulateSample simulation

Description

Simulate count data for one sample from a fictional single-cell RNA-seq experiment using the Splat method.

Usage

splatPopSimulateSample(
  params = newSplatPopParams(),
  method = c("single", "groups", "paths"),
  batch = "batch1",
  counts.only = FALSE,
  verbose = TRUE,
  sample.means,
  ...
)

Arguments

params	SplatPopParams object containing parameters for population scale simulations. See SplatPopParams for details.
method	which simulation method to use. Options are "single" which produces a single population, "groups" which produces distinct groups (eg. cell types), "paths" which selects cells from continuous trajectories (eg. differentiation processes).
batch	Batch number.
counts.only	logical. Whether to return only the counts.
verbose	logical. Whether to print progress messages.
sample.means	Gene means to use if running splatSimulatePop().
...	any additional parameter settings to override what is provided in params.

Details

This function closely mirrors splatSimulate. The main difference is that it takes the means simulated by splatPopSimulateMeans instead of randomly sampling a mean for each gene. For details about this function see the documentation for splatSimulate.

Value

SingleCellExperiment object containing the simulated counts and intermediate values for one sample.

See Also

splatSimLibSizes, splatPopSimGeneMeans, splatSimBatchEffects, splatSimBatchCellMeans, splatSimDE, splatSimCellMeans, splatSimBCVMeans, splatSimTrueCounts, splatSimDropout, splatPopSimulateSC

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