Kersplat sample

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

Value

SingleCellExperiment object containing the simulated counts and intermediate values.

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.

See also

kersplatSimLibSizes, kersplatSimCellMeans, kersplatSimCellCounts, kersplatSimAmbientCounts, kersplatSimCounts

Examples

if (requireNamespace("igraph", quietly = TRUE)) {
    params <- kersplatSetup()
    sim <- kersplatSample(params)
}
#> Setting up parameters...
#> Generating gene network...
#> Selecting regulators...
#> Simulating means...
#> Sampling from gamma distribution...
#> Simulating paths...
#> Simulating path 1...
#> Creating simulation object...
#> Simulating library sizes...
#> Sampling from log-normal distribution...
#> Assigning cells to paths...
#> Assigning cells to steps...
#> Simulating cell means...
#> Applying BCV adjustment...
#> Simulating cell counts...
#> Simulating ambient counts...
#> Simulating final counts...
#> Sparsifying assays...
#> Automatically converting to sparse matrices, threshold = 0.95
#> Skipping 'CellMeans': estimated sparse size 1.49 * dense matrix
#> Skipping 'CellCounts': estimated sparse size 1.66 * dense matrix
#> Converting 'AmbientCounts' to sparse matrix: estimated sparse size 0.43 * dense matrix
#> Skipping 'counts' as it is already a dgCMatrix