R/lun-estimate.R

In Oshlack/splatter: Simple Simulation of Single-cell RNA Sequencing Data

#' Estimate Lun simulation parameters
#'
#' Estimate simulation parameters for the Lun simulation from a real dataset.
#'
#' @param counts either a counts matrix or an SingleCellExperiment object
#'        containing count data to estimate parameters from.
#' @param params LunParams object to store estimated values in.
#'
#' @details
#' The \code{nGenes} and \code{nCells} parameters are taken from the size of the
#' input data. No other parameters are estimated. See \code{\link{LunParams}}
#' for more details on the parameters.
#'
#' @return LunParams object containing the estimated parameters.
#'
#' @examples
#' # Load example data
#' library(scuttle)
#' set.seed(1)
#' sce <- mockSCE()
#'
#' params <- lunEstimate(sce)
#' params
#' @export
lunEstimate <- function(counts, params = newLunParams()) {
    UseMethod("lunEstimate")
}

#' @rdname lunEstimate
#' @export
lunEstimate.SingleCellExperiment <- function(counts, params = newLunParams()) {
    counts <- getCounts(counts)
    lunEstimate(counts, params)
}

#' @rdname lunEstimate
#' @export
lunEstimate.matrix <- function(counts, params = newLunParams()) {
    checkmate::assertClass(params, "LunParams")

    params <- setParams(
        params,
        nGenes = nrow(counts),
        groupCells = ncol(counts)
    )

    return(params)
}