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 15 cells). Default: `WithBatch = FALSE`.
`WithSpikes` | If `TRUE`, the simulated dataset contains 20 spike-in genes. If `WithSpikes = FALSE`, `WithBatch` is automatically set to `TRUE`. Default: `WithSpikes = TRUE`

### Details

Note: In BASiCS versions < 1.5.22, `makeExampleBASiCS_Data` used a fixed seed within the function. This has been removed to comply with Bioconductor policies. If a reproducible example is required, please use `set.seed` prior to calling `makeExampleBASiCS_Data` .

### 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 30 cells. Alternatively, it contains 50 biological genes and 30 cells.

### Author(s)

Catalina A. Vallejos cnvallej@uc.cl

Nils Eling eling@ebi.ac.uk

### Examples

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

[Package BASiCS version 1.8.1 Index]