Estimate Lun simulation parameters

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

Usage

lunEstimate(counts, params = newLunParams())

# S3 method for class 'SingleCellExperiment'
lunEstimate(counts, params = newLunParams())

# S3 method for class 'matrix'
lunEstimate(counts, params = newLunParams())

Arguments

counts

either a counts matrix or an SingleCellExperiment object containing count data to estimate parameters from.

params

LunParams object to store estimated values in.

Value

LunParams object containing the estimated parameters.

Details

The nGenes and nCells parameters are taken from the size of the input data. No other parameters are estimated. See LunParams for more details on the parameters.

Examples

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

params <- lunEstimate(sce)
params
#> A Params object of class LunParams 
#> Parameters can be (estimable) or [not estimable], 'Default' or  'NOT DEFAULT' 
#> Secondary parameters are usually set during simulation
#> 
#> Global: 
#> (GENES)  (CELLS)   [SEED] 
#>    2000      200   787110 
#> 
#> 9 additional parameters 
#> 
#> Mean: 
#>  [Rate]  [Shape] 
#>       2        2 
#> 
#> Counts: 
#> [Dispersion] 
#>          0.1 
#> 
#> Groups: 
#>      [GROUPS]  [GROUP CELLS] 
#>             1            200 
#> 
#> Diff expr: 
#>   [Genes]  [Up Prop]    [Up FC]  [Down FC] 
#>      1000        0.5          5          0 
#>