BASiCSParams {splatter} | R Documentation

## The BASiCSParams class

### Description

S4 class that holds parameters for the BASiCS simulation.

### Parameters

The BASiCS 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.

Batch parameters
  `nBatches`

    Number of batches to simulate.

  `batchCells`

    Number of cells in each batch.

Gene parameters
  `gene.params`

    A `data.frame` containing gene parameters with two coloumns: `Mean` (mean expression for each biological gene) and `Delta` (cell-to-cell heterogeneity for each biological gene).

Spike-in parameters
  `nSpikes`

    The number of spike-ins to simulate.

  `spike.means`

    Input molecules for each spike-in.

Cell parameters
  `cell.params`

    A `data.frame` containing gene parameters with two coloumns: `Phi` (mRNA content factor for each cell, scaled to sum to the number of cells in each batch) and `S` (capture efficient for each cell).

Variability parameters
  `theta`

    Technical variability parameter for each batch.

The parameters not shown in brackets can be estimated from real data using `BASiCSEstimate`. For details of the BASiCS simulation see `BASiCSSimulate`.

[Package splatter version 1.4.3 Index]