Estimate simulation parameters for the Lun simulation from a real dataset.
lunEstimate(counts, params = newLunParams()) # S3 method for SingleCellExperiment lunEstimate(counts, params = newLunParams()) # S3 method for matrix lunEstimate(counts, params = newLunParams())
counts | either a counts matrix or an SingleCellExperiment object containing count data to estimate parameters from. |
---|---|
params | LunParams object to store estimated values in. |
LunParams object containing the estimated parameters.
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.
#> Warning: package ‘scater’ was built under R version 3.6.1#>#> A Params object of class LunParams #> Parameters can be (estimable) or [not estimable], 'Default' or 'NOT DEFAULT' #> #> Global: #> (GENES) (CELLS) [Seed] #> 2000 200 848036 #> #> 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 #>