splatPopSimulate: splatPop simulation
In splatter: Simple Simulation of Single-cell RNA Sequencing Data

Description Usage Arguments Details Value See Also Examples

Simulate scRNA-seq count data using the splat model for a population of individuals with correlation structure.

splatPopSimulate(
  params = newSplatPopParams(nGenes = 1000),
  vcf = mockVCF(),
  method = c("single", "groups", "paths"),
  gff = NULL,
  key = NULL,
  counts.only = FALSE,
  sparsify = TRUE,
  verbose = TRUE,
  ...
)

`params`	SplatPopParams object containing parameters for population scale simulations. See `SplatPopParams` for details.
`vcf`	VariantAnnotation object containing genotypes of samples.
`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).
`gff`	Either NULL or a data.frame object containing a GFF/GTF file.
`key`	Either NULL or a data.frame object containing a full or partial splatPop key.
`counts.only`	logical. Whether to save only counts in sce object.
`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`.

This functions is for simulating data in a single step. It consists of a call to splatPopSimulateMeans, which simulates a mean expression level per gene per sample, followed by a call to splatPopSimulateSC, which uses the splat model to simulate single-cell counts per individual. Please see the documentation for those functions for more details.

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.

splatPopSimulateMeans, splatPopSimulateSC

if (requireNamespace("VariantAnnotation", quietly = TRUE) &&
    requireNamespace("preprocessCore", quietly = TRUE)) {
    sim <- splatPopSimulate()
}