LunParams: The LunParams class

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

Description

S4 class that holds parameters for the Lun simulation.

Parameters

The Lun simulation uses the following parameters:

nGenes

The number of genes to simulate.

nCells

The number of cells to simulate.

[nGroups]

The number of groups to simulate.

[groupCells]

Vector giving the number of cells in each simulation group/path.

[seed]

Seed to use for generating random numbers.

Mean parameters

[mean.shape]

Shape parameter for the mean gamma distribution.

[mean.rate]

Rate parameter for the mean gamma distribution.

Counts parameters

[count.disp]

The dispersion parameter for the counts negative binomial distribution.

Differential expression parameters

[de.nGenes]

The number of genes that are differentially expressed in each group

[de.upProp]

The proportion of differentially expressed genes that are up-regulated in each group

[de.upFC]

The fold change for up-regulated genes

[de.downFC]

The fold change for down-regulated genes

The parameters not shown in brackets can be estimated from real data using lunEstimate. For details of the Lun simulation see lunSimulate.

splatter documentation built on Dec. 3, 2020, 2:01 a.m.