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())
counts | either a counts matrix or a SingleCellExperiment object containing count data to estimate parameters from. |
---|---|
params | SimpleParams object to store estimated values in. |
SimpleParams object containing the estimated parameters.
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.
# Load example data library(scater) 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 42837 #> #> 3 additional parameters #> #> Mean: #> (RATE) (SHAPE) #> 0.0008052293183292 0.131835949613878 #> #> Counts: #> [Dispersion] #> 0.1 #>