% Generated by roxygen2: do not edit by hand % Please edit documentation in R/scDD-estimate.R \name{scDDEstimate} \alias{scDDEstimate} \alias{scDDEstimate.SCESet} \alias{scDDEstimate.matrix} \title{Estimate scDD simulation parameters} \usage{ scDDEstimate(counts, conditions, params = newSCDDParams(), verbose = TRUE, BPPARAM = SerialParam()) \method{scDDEstimate}{SCESet}(counts, conditions, params = newSCDDParams(), verbose = TRUE, BPPARAM = SerialParam()) \method{scDDEstimate}{matrix}(counts, conditions, params = newSCDDParams(), verbose = TRUE, BPPARAM = SerialParam()) } \arguments{ \item{counts}{either a counts matrix or an SCESet object containing count data to estimate parameters from.} \item{conditions}{Vector giving the condition that each cell belongs to. Conditions can be 1 or 2.} \item{params}{SCDDParams object to store estimated values in.} \item{verbose}{logical. Whether to show progress messages.} \item{BPPARAM}{A \code{\link[BiocParallel]{BiocParallelParam}} instance giving the parallel back-end to be used. Default is \code{\link[BiocParallel]{SerialParam}} which uses a single core.} } \value{ SCDDParams object containing the estimated parameters. } \description{ Estimate simulation parameters for the scDD simulation from a real dataset. } \details{ This function applies \code{\link[scDD]{preprocess}} to the counts then uses \code{\link[scDD]{scDD}} to estimate the numbers of each gene type to simulate. The output is then converted to a SCDDParams object. See \code{\link[scDD]{preprocess}} and \code{\link[scDD]{scDD}} for details. } \examples{ \dontrun{ data("sc_example_counts") conditions <- sample(1:2, ncol(sc_example_counts), replace = TRUE) params <- scDDEstimate(sc_example_counts, conditions) params } }