lun2Estimate {splatter} | R Documentation

## Estimate Lun2 simulation parameters

### Description

Estimate simulation parameters for the Lun2 simulation from a real dataset.

### Usage

    lun2Estimate(counts, plates, params = newLun2Params(), min.size = 200,
      verbose = TRUE, BPPARAM = SerialParam())

    ## S3 method for class 'SingleCellExperiment'
    lun2Estimate(counts, plates,
      params = newLun2Params(), min.size = 200, verbose = TRUE,
      BPPARAM = SerialParam())

    ## S3 method for class 'matrix'
    lun2Estimate(counts, plates, params = newLun2Params(),
      min.size = 200, verbose = TRUE, BPPARAM = SerialParam())

### Arguments

`counts` | either a counts matrix or a SingleCellExperiment object containing count data to estimate parameters from.
`plates` | integer vector giving the plate that each cell originated from.
`params` | Lun2Params object to store estimated values in.
`min.size` | minimum size of clusters when identifying group of cells in the data.
`verbose` | logical. Whether to show progress messages.
`BPPARAM` | A `BiocParallelParam` instance giving the parallel back-end to be used. Default is `SerialParam` which uses a single core.

### Details

See `Lun2Params` for more details on the parameters.

### Value

LunParams object containing the estimated parameters.

### Examples

    ## Not run:
    # Load example data
    library(scater)
    data("sc_example_counts")
    data("sc_example_cell_info")

    plates <- factor(sc_example_cell_info$Mutation_Status)
    params <- lun2Estimate(sc_example_counts, plates, min.size = 20)
    params

    ## End(Not run)

[Package splatter version 1.8.0 Index]