Estimate PhenoPath simulation parameters

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

Usage

phenoEstimate(counts, params = newPhenoParams())

# S3 method for class 'SingleCellExperiment'
phenoEstimate(counts, params = newPhenoParams())

# S3 method for class 'matrix'
phenoEstimate(counts, params = newPhenoParams())

Arguments

counts

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

params

PhenoParams object to store estimated values in.

Value

PhenoParams object containing the estimated parameters.

Details

The nGenes and nCells parameters are taken from the size of the input data. The total number of genes is evenly divided into the four types. See PhenoParams for more details on the parameters.

Examples

if (requireNamespace("phenopath", quietly = TRUE)) {
    # Load example data
    library(scuttle)
    set.seed(1)
    sce <- mockSCE()

    params <- phenoEstimate(sce)
    params
}
#> A Params object of class PhenoParams 
#> 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 
#> 
#> 4 additional parameters 
#> 
#> Genes: 
#>              [DE]              [PST]       [PST + BETA]  [DE + PST + BETA] 
#>               500                500                500                500 
#>