splatPopSimulate {splatter} | R Documentation

## splatPop simulation

### Description

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

### Usage

    splatPopSimulate(
      params = newSplatPopParams(nGenes = 50),
      vcf = mockVCF(),
      method = c("single", "groups", "paths"),
      gff = NULL,
      eqtl = NULL,
      means = NULL,
      key = NULL,
      counts.only = FALSE,
      sparsify = TRUE,
      verbose = TRUE,
      ...
    )

### Arguments

`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.
`eqtl` | Either NULL or if simulating population parameters directly from empirical data, a data.frame with empirical/desired eQTL results. To see required format, run 'mockEmpiricalSet()' and see eqtl output.
`means` | Either NULL or if simulating population parameters directly from empirical data, a Matrix of real gene means across a population, where each row is a gene and each column is an individual in the population. To see required format, run 'mockEmpiricalSet()' and see means output.
`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`.

### Details

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.

### 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.

### See Also

`splatPopSimulateMeans`, `splatPopSimulateSC`

### Examples

    if (requireNamespace("VariantAnnotation", quietly = TRUE) &&
        requireNamespace("preprocessCore", quietly = TRUE)) {
        vcf <- mockVCF()
        gff <- mockGFF()
        sim <- splatPopSimulate(vcf = vcf, gff = gff, sparsify = FALSE)
    }

[Package splatter version 1.18.2 Index]