The Lun2Params class

S4 class that holds parameters for the Lun2 simulation.

Parameters

The Lun2 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.

Gene parameters

gene.params

A data.frame containing gene parameters with two columns: Mean (mean expression for each gene) and Disp (dispersion for each gene).

zi.params

A data.frame containing zero-inflated gene parameters with three columns: Mean (mean expression for each gene), Disp (dispersion for each, gene), and Prop (zero proportion for each gene).

[nPlates]

The number of plates to simulate.

Plate parameters

plate.ingroup

Character vector giving the plates considered to be part of the "ingroup".

plate.mod

Plate effect modifier factor. The plate effect variance is divided by this value.

plate.var

Plate effect variance.

Cell parameters

cell.plates

Factor giving the plate that each cell comes from.

cell.libSizes

Library size for each cell.

cell.libMod

Modifier factor for library sizes. The library sizes are multiplied by this value.

Differential expression parameters

de.nGenes

Number of differentially expressed genes.

de.fc

Fold change for differentially expressed genes.

The parameters not shown in brackets can be estimated from real data using lun2Estimate. For details of the Lun2 simulation see lun2Simulate.