splatSimulate: Splat simulation

In Oshlack/splatter: Simple Simulation of Single-cell RNA Sequencing Data

Splat simulation

Description

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

Usage

splatSimulate(
  params = newSplatParams(),
  method = c("single", "groups", "paths"),
  sparsify = TRUE,
  verbose = TRUE,
  ...
)

splatSimulateSingle(params = newSplatParams(), verbose = TRUE, ...)

splatSimulateGroups(params = newSplatParams(), verbose = TRUE, ...)

splatSimulatePaths(params = newSplatParams(), verbose = TRUE, ...)

Arguments

params	SplatParams object containing parameters for the simulation. See SplatParams for details.
method	which simulation method to use. Options are "single" which produces a single population, "groups" which produces distinct groups (eg. cell types), or "paths" which selects cells from continuous trajectories (eg. differentiation processes).
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

Parameters can be set in a variety of ways. If no parameters are provided the default parameters are used. Any parameters in params can be overridden by supplying additional arguments through a call to setParams. This design allows the user flexibility in how they supply parameters and allows small adjustments without creating a new SplatParams object. See examples for a demonstration of how this can be used.

The simulation involves the following steps:

1. Set up simulation object

2. Simulate library sizes

3. Simulate gene means

4. Simulate groups/paths

5. Simulate BCV adjusted cell means

6. Simulate true counts

7. Simulate dropout

8. Create final dataset

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.

Group

The group or path the cell belongs to.

ExpLibSize

The expected library size for that cell.

Step (paths only)

how far along the path each cell is.

rowData

Gene

Unique gene identifier.

BaseGeneMean

The base expression level for that gene.

OutlierFactor

Expression outlier factor for that gene. Values of 1 indicate the gene is not an expression outlier.

GeneMean

Expression level after applying outlier factors.

BatchFac[Batch]

The batch effects factor for each gene for a particular batch.

DEFac[Group]

The differential expression factor for each gene in a particular group. Values of 1 indicate the gene is not differentially expressed.

SigmaFac[Path]

Factor applied to genes that have non-linear changes in expression along a path.

assays

BatchCellMeans

The mean expression of genes in each cell after adding batch effects.

BaseCellMeans

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

BCV

The Biological Coefficient of Variation for each gene in each cell.

CellMeans

The mean expression level of genes in each cell adjusted for BCV.

TrueCounts

The simulated counts before dropout.

Dropout

Logical matrix showing which values have been dropped in which cells.

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.

References

Zappia L, Phipson B, Oshlack A. Splatter: simulation of single-cell RNA sequencing data. Genome Biology (2017).

Paper: 10.1186/s13059-017-1305-0

Code: https://github.com/Oshlack/splatter

See Also

splatSimLibSizes, splatSimGeneMeans, splatSimBatchEffects, splatSimBatchCellMeans, splatSimDE, splatSimCellMeans, splatSimBCVMeans, splatSimTrueCounts, splatSimDropout

Examples

# Simulation with default parameters
sim <- splatSimulate()


# Simulation with different number of genes
sim <- splatSimulate(nGenes = 1000)
# Simulation with custom parameters
params <- newSplatParams(nGenes = 100, mean.rate = 0.5)
sim <- splatSimulate(params)
# Simulation with adjusted custom parameters
sim <- splatSimulate(params, mean.rate = 0.6, out.prob = 0.2)
# Simulate groups
sim <- splatSimulate(method = "groups")
# Simulate paths
sim <- splatSimulate(method = "paths")

Oshlack/splatter documentation built on Dec. 10, 2024, 3:48 p.m.