splatPopSimulateSC {splatter} | R Documentation

## splatPopSimulateSC

### Description

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

### Usage

    splatPopSimulateSC(
      sim.means,
      params,
      key,
      method = c("single", "groups", "paths"),
      counts.only = FALSE,
      sparsify = TRUE,
      verbose = TRUE,
      ...
    )

### Arguments

`sim.means` | Matrix or list of matrices of gene means for the population. Output from 'splatPopSimulateMeans()'.
`params` | SplatPopParams object containing parameters for population scale simulations. See `SplatPopParams` for details.
`key` | data.frame object containing a full or partial splatPop key. Output from 'splatPopSimulateMeans()'.
`method` | which simulation method to use. Options are "single" which produces a single cell population for each sample, "groups" which produces distinct groups (eg. cell types) for each sample (note, this creates separate groups from those created in 'popSimulate' with only DE effects), and "paths" which selects cells from continuous trajectories (eg. differentiation processes).
`counts.only` | logical. Whether to return only the counts.
`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`.

### Value

SingleCellExperiment object containing simulated counts, intermediate values like the gene means simulated in 'splatPopSimulateMeans', and information about the differential expression and eQTL effects assigned to each gene.

### Examples

    if (requireNamespace("VariantAnnotation", quietly = TRUE) &&
        requireNamespace("preprocessCore", quietly = TRUE)) {
        params <- newSplatPopParams()
        sim.means <- splatPopSimulateMeans()
        sim <- splatPopSimulateSC(sim.means$means, params, sim.means$key)
    }

[Package splatter version 1.14.1 Index]