makeExampleBASiCS_Data {BASiCS} | R Documentation

## Create a synthetic SingleCellExperiment example object with the format required for BASiCS

### Description

A synthetic `SingleCellExperiment` object is generated by simulating a dataset from the model underlying BASiCS. This is used to illustrate BASiCS in some of the package and vignette examples.

### Usage

    makeExampleBASiCS_Data(WithBatch = FALSE, WithSpikes = TRUE)

### Arguments

`WithBatch` | If `TRUE`, 2 batches are generated (each of them containing 10 cells). Default: `WithBatch = FALSE`.
`WithSpikes` | If `TRUE`, the simulated dataset contains 20 spike-in genes. Default: `WithSpikes` `= TRUE`.

### Value

An object of class `SingleCellExperiment`, with synthetic data simulated from the model implemented in BASiCS. If `WithSpikes = TRUE`, it contains 70 genes (50 biological and 20 spike-in) and 20 cells. Alternatively, it contains 50 biological genes and 20 cells.

### Author(s)

Catalina A. Vallejos cnvallej@uc.cl and Nils Eling

### References

Vallejos, Marioni and Richardson (2015). PLoS Computational Biology.

Vallejos, Marioni and Richardson (2016). Genome Biology.

### Examples

    Data <- makeExampleBASiCS_Data()
    is(Data, 'SingleCellExperiment')

[Package BASiCS version 1.0.1 Index]