lun2Estimate {splatter} | R Documentation |
Estimate simulation parameters for the Lun2 simulation from a real dataset.
lun2Estimate( counts, plates, params = newLun2Params(), min.size = 200, verbose = TRUE, BPPARAM = SerialParam() ) ## S3 method for class 'SingleCellExperiment' lun2Estimate( counts, plates, params = newLun2Params(), min.size = 200, verbose = TRUE, BPPARAM = SerialParam() ) ## S3 method for class 'matrix' lun2Estimate( counts, plates, params = newLun2Params(), min.size = 200, verbose = TRUE, BPPARAM = SerialParam() )
counts |
either a counts matrix or a SingleCellExperiment object containing count data to estimate parameters from. |
plates |
integer vector giving the plate that each cell originated from. |
params |
Lun2Params object to store estimated values in. |
min.size |
minimum size of clusters when identifying group of cells in the data. |
verbose |
logical. Whether to show progress messages. |
BPPARAM |
A |
See Lun2Params
for more details on the parameters.
LunParams object containing the estimated parameters.
## Not run: # Load example data library(scater) set.seed(1) sce <- mockSCE() plates <- as.numeric(factor(colData(sce)$Mutation_Status)) params <- lun2Estimate(sce, plates, min.size = 20) params ## End(Not run)