Lun2Params {splatter} | R Documentation

## The Lun2Params class

### Description

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 coloumns: `Mean` (mean expression for each gene) and `Disp` (dispersion for each gene).

  `zi.params`

    A `data.frame` containing zero-inflated gene parameters with three coloumns: `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 vecotor 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`.

[Package splatter version 1.4.3 Index]