SCDDParams: The SCDDParams class

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

The SCDDParams class

Description

S4 class that holds parameters for the scDD simulation.

Parameters

The SCDD simulation uses the following parameters:

nGenes

The number of genes to simulate (not used).

nCells

The number of cells to simulate in each condition.

[seed]

Seed to use for generating random numbers.

SCdat

SingleCellExperiment containing real data.

nDE

Number of DE genes to simulate.

nDP

Number of DP genes to simulate.

nDM

Number of DM genes to simulate.

nDB

Number of DB genes to simulate.

nEE

Number of EE genes to simulate.

nEP

Number of EP genes to simulate.

[sd.range]

Interval for fold change standard deviations.

[modeFC]

Values for DP, DM and DB mode fold changes.

[varInflation]

Variance inflation factors for each condition. If all equal to 1 will be set to NULL (default).

[condition]

String giving the column that represents biological group of interest.

The parameters not shown in brackets can be estimated from real data using scDDEstimate. See simulateSet for more details about the parameters. For details of the Splatter implementation of the scDD simulation see scDDSimulate.

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