Add lunEstimate function

DESCRIPTION

 Package: splatter
 Type: Package
 Title: Simple Simulation of Single-cell RNA Sequencing Data
-Version: 0.6.11
+Version: 0.6.12
 Date: 2016-10-14
 Author: Luke Zappia
 Authors@R: as.person(c(

R/SimpleParams-methods.R

@@ -36,7 +36,7 @@ setMethod("show", "SimpleParams", function(object) {
                              "(Shape)"      = "mean.shape"),
                "Counts:" = c("[Dispersion]" = "count.disp"))
 
-    # Mean parameters aren't estiamated for the LunParams object which
+    # Mean parameters aren't estimated for the LunParams object which
     # inherits from SimpleParams
     if (class(object) == "LunParams") {
         pp[["Mean:"]] <- c("[Rate]" = "mean.rate", "[Shape]" = "mean.shape")

R/lun-estimate.R

+#' Estimate Lun simulation parameters
+#'
+#' Estimate simulation parameters for the Lun simulation from a real dataset.
+#'
+#' @param counts either a counts matrix or an SCESet 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
+#' data("sc_example_counts")
+#' params <- lunEstimate(sc_example_counts)
+#' params
+#' @export
+lunEstimate <- function(counts, params = newLunParams()) {
+    UseMethod("lunEstimate")
+}
+
+#' @rdname lunEstimate
+#' @export
+lunEstimate.SCESet <- function(counts, params = newLunParams()) {
+    counts <- scater::counts(counts)
+    lunEstimate(counts, params)
+}
+
+#' @rdname lunEstimate
+#' @importFrom stats median
+#' @export
+lunEstimate.matrix <- function(counts, params = newLunParams()) {
+
+    checkmate::assertClass(params, "LunParams")
+
+    params <- setParams(params, nGenes = nrow(counts),
+                        groupCells = ncol(counts))
+
+    return(params)
+}
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