S4 class that holds parameters for the BASiCS simulation.
Parameters
The BASiCS simulation uses the following parameters:
nGenesThe number of genes to simulate.
nCellsThe number of cells to simulate.
[seed]Seed to use for generating random numbers.
- Batch parameters
nBatchesNumber of batches to simulate.
batchCellsNumber of cells in each batch.
- Gene parameters
gene.paramsA
data.framecontaining gene parameters with two columns:Mean(mean expression for each biological gene) andDelta(cell-to-cell heterogeneity for each biological gene).
- Spike-in parameters
nSpikesThe number of spike-ins to simulate.
spike.meansInput molecules for each spike-in.
- Cell parameters
cell.paramsA
data.framecontaining gene parameters with two columns:Phi(mRNA content factor for each cell, scaled to sum to the number of cells in each batch) andS(capture efficient for each cell).
- Variability parameters
thetaTechnical 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.