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

phenoEstimate(counts, params = newPhenoParams())

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

# S3 method for 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

data("sc_example_counts") params <- phenoEstimate(sc_example_counts) params
#> A Params object of class PhenoParams #> Parameters can be (estimable) or [not estimable], 'Default' or 'NOT DEFAULT'. #> #> Global: #> (GENES) (CELLS) [Seed] #> 2000 40 736969 #> #> 4 additional parameters #> #> Genes: #> [DE] [PST] [PST + BETA] [DE + PST + BETA] #> 500 500 500 500 #>