Estimate simulation parameters for the mfa simulation from a real dataset.
mfaEstimate(counts, params = newMFAParams()) # S3 method for SingleCellExperiment mfaEstimate(counts, params = newMFAParams()) # S3 method for matrix mfaEstimate(counts, params = newMFAParams())
counts | either a counts matrix or a SingleCellExperiment object containing count data to estimate parameters from. |
---|---|
params | MFAParams object to store estimated values in. |
MFAParams object containing the estimated parameters.
The nGenes
and nCells
parameters are taken from the size of the
input data. The dropout lambda parameter is estimate using
empirical_lambda
. See MFAParams
for more
details on the parameters.
# Load example data library(scater) data("sc_example_counts") params <- mfaEstimate(sc_example_counts) params#> A Params object of class MFAParams #> Parameters can be (estimable) or [not estimable], 'Default' or 'NOT DEFAULT' #> #> Global: #> (GENES) (CELLS) [Seed] #> 2000 40 171612 #> #> 4 additional parameters #> #> Transient: #> [Proportion] #> 0 #> #> Negative: #> [Zero] #> TRUE #> #> Dropout: #> [Present] (LAMBDA) #> FALSE 0.00352186231063193 #>