makeExampleBASiCS_Data: Create a synthetic SingleCellExperiment example object with...

In catavallejos/BASiCS: Bayesian Analysis of Single-Cell Sequencing data

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 [e-mail]

Nils Eling [e-mail]

Examples

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

catavallejos/BASiCS documentation built on March 27, 2024, 12:49 a.m.