simpleEstimate {splatter} | R Documentation

## Estimate simple simulation parameters

### Description

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

### Usage

    simpleEstimate(counts, params = newSimpleParams())

    ## S3 method for class 'SingleCellExperiment'
    simpleEstimate(counts, params = newSimpleParams())

    ## S3 method for class 'matrix'
    simpleEstimate(counts, params = newSimpleParams())

### Arguments

`counts` | either a counts matrix or a SingleCellExperiment object containing count data to estimate parameters from.
`params` | SimpleParams object to store estimated values in.

### Details

The `nGenes` and `nCells` parameters are taken from the size of the input data. The mean parameters are estimated by fitting a gamma distribution to the library size normalised mean expression level using `fitdist`. See `SimpleParams` for more details on the parameters.

### Value

SimpleParams object containing the estimated parameters.

### Examples

    # Load example data
    library(scater)
    set.seed(1)
    sce <- mockSCE()

    params <- simpleEstimate(sce)
    params

[Package splatter version 1.11.4 Index]