kersplatSample {splatter} | R Documentation

## Kersplat sample

### Description

Sample cells for the Kersplat simulation

### Usage

    kersplatSample(params, sparsify = TRUE, verbose = TRUE)

### Arguments

`params` | KersplatParams 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

### Details

The second stage is a two-step Kersplat simulation is to generate cells based on a complete `KersplatParams` object. intermediate parameters.

The sampling process involves the following steps:

1. Simulate library sizes for each cell

2. Simulate means for each cell

3. Simulate endogenous counts for each cell

4. Simulate ambient counts for each cell

5. Simulate final counts for each cell

The final output is a `SingleCellExperiment` object that contains the simulated counts but also the values for various intermediate steps. These are stored in the `colData` (for cell specific information), `rowData` (for gene specific information) or `assays` (for gene by cell matrices) slots. This additional information includes:

`colData`
  Cell

    Unique cell identifier.

  Type

    Whether the cell is a Cell, Doublet or Empty.

  CellLibSize

    The expected number of endogenous counts for that cell.

  AmbientLibSize

    The expected number of ambient counts for that cell.

  Path

    The path the cell belongs to.

  Step

    How far along the path each cell is.

  Path1

    For doublets the path of the first partner in the doublet (otherwise `NA`).

  Step1

    For doublets the step of the first partner in the doublet (otherwise `NA`).

  Path2

    For doublets the path of the second partner in the doublet (otherwise `NA`).

  Step2

    For doublets the step of the second partner in the doublet (otherwise `NA`).

`rowData`
  Gene

    Unique gene identifier.

  BaseMean

    The base expression level for that gene.

  AmbientMean

    The ambient expression level for that gene.

`assays`
  CellMeans

    The mean expression of genes in each cell after any differential expression and adjusted for expected library size.

  CellCounts

    Endogenous count matrix.

  AmbientCounts

    Ambient count matrix.

  counts

    Final count matrix.

Values that have been added by Splatter are named using `UpperCamelCase` in order to differentiate them from the values added by analysis packages which typically use `underscore_naming`.

### Value

SingleCellExperiment object containing the simulated counts and intermediate values.

### See Also

`kersplatSimLibSizes`, `kersplatSimCellMeans`, `kersplatSimCellCounts`, `kersplatSimAmbientCounts`, `kersplatSimCounts`

### Examples

    if (requireNamespace("igraph", quietly = TRUE)) {
        params <- kersplatSetup()
        sim <- kersplatSample(params)
    }

[Package splatter version 1.14.1 Index]