PhenoParams: The PhenoParams class

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

The PhenoParams class

Description

S4 class that holds parameters for the PhenoPath simulation.

Parameters

The PhenoPath 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.

[n.de]

Number of genes to simulate from the differential expression regime

[n.pst]

Number of genes to simulate from the pseudotime regime

[n.pst.beta]

Number of genes to simulate from the pseudotime + beta interactions regime

[n.de.pst.beta]

Number of genes to simulate from the differential expression + pseudotime + interactions regime

The parameters not shown in brackets can be estimated from real data using phenoEstimate. For details of the PhenoPath simulation see phenoSimulate.

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