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

simpleEstimate(counts, params = newSimpleParams())

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

# S3 method for 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.

Value

SimpleParams object containing the estimated parameters.

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.

Examples

data("sc_example_counts") params <- simpleEstimate(sc_example_counts) params
#> A Params object of class SimpleParams #> Parameters can be (estimable) or [not estimable], 'Default' or 'NOT DEFAULT'. #> #> Global: #> (GENES) (CELLS) [Seed] #> 2000 40 213034 #> #> 3 additional parameters #> #> Mean: #> (RATE) (SHAPE) #> 0.0008052293183292 0.131835949613878 #> #> Counts: #> [Dispersion] #> 0.1 #>