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

scDDEstimate(counts, conditions, params = newSCDDParams(), verbose = TRUE,
  BPPARAM = SerialParam())

# S3 method for SingleCellExperiment
scDDEstimate(counts, conditions,
  params = newSCDDParams(), verbose = TRUE, BPPARAM = SerialParam())

# S3 method for matrix
scDDEstimate(counts, conditions, params = newSCDDParams(),
  verbose = TRUE, BPPARAM = SerialParam())

Arguments

counts

either a counts matrix or a SingleCellExperiment object containing count data to estimate parameters from.

conditions

Vector giving the condition that each cell belongs to. Conditions can be 1 or 2.

params

SCDDParams object to store estimated values in.

verbose

logical. Whether to show progress messages.

BPPARAM

A BiocParallelParam instance giving the parallel back-end to be used. Default is SerialParam which uses a single core.

Value

SCDDParams object containing the estimated parameters.

Details

This function applies preprocess to the counts then uses scDD to estimate the numbers of each gene type to simulate. The output is then converted to a SCDDParams object. See preprocess and scDD for details.

Examples

# NOT RUN {
data("sc_example_counts")
conditions <- sample(1:2, ncol(sc_example_counts), replace = TRUE)
params <- scDDEstimate(sc_example_counts, conditions)
params
# }