MFAParams: The MFAParams class

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

The MFAParams class

Description

S4 class that holds parameters for the mfa simulation.

Parameters

The mfa simulation uses the following parameters:

nGenes

The number of genes to simulate.

nCells

The number of cells to simulate.

[seed]

Seed to use for generating random numbers.

[trans.prop]

Proportion of genes that show transient expression. These genes are briefly up or down-regulated before returning to their initial state

[zero.neg]

Logical. Whether to set negative expression values to zero. This will zero-inflate the data.

[dropout.present]

Logical. Whether to simulate dropout.

dropout.lambda

Lambda parameter for the exponential dropout function.

The parameters not shown in brackets can be estimated from real data using mfaEstimate. See create_synthetic for more details about the parameters. For details of the Splatter implementation of the mfa simulation see mfaSimulate.

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