Update SCDDParams

R/AllClasses.R

@@ -409,7 +409,7 @@ setClass("Lun2Params",
 #'     \item{\code{nCells}}{The number of cells to simulate in each condition.}
 #'     \item{\code{[seed]}}{Seed to use for generating random numbers.}
 #'     \item{\code{SCdat}}{
-#'     \code{\link[SummarizedExperiment]{SummarizedExperiment}} containing real
+#'     \code{\link[SingleCellExperiment]{SingleCellExperiment}} containing real
 #'     data.}
 #'     \item{\code{nDE}}{Number of DE genes to simulate.}
 #'     \item{\code{nDP}}{Number of DP genes to simulate.}
@@ -427,8 +427,8 @@ setClass("Lun2Params",
 #'
 #' The parameters not shown in brackets can be estimated from real data using
 #' \code{\link{scDDEstimate}}. See \code{\link[scDD]{simulateSet}} for more
-#' details of the parameters. For details of the Splatter implementation of the
-#' scDD simulation see \code{\link{scDDSimulate}}.
+#' details about the parameters. For details of the Splatter implementation of
+#' the scDD simulation see \code{\link{scDDSimulate}}.
 #'
 #' @name SCDDParams
 #' @rdname SCDDParams
@@ -448,7 +448,7 @@ setClass("SCDDParams",
                    varInflation = "numeric",
                    condition = "character"),
           prototype = prototype(SCdat =
-                                   SummarizedExperiment::SummarizedExperiment(),
+                                   SingleCellExperiment::SingleCellExperiment(),
                                nCells = 100,
                                nDE = 250,
                                nDP = 250,

R/SCDDParams-methods.R

@@ -26,7 +26,7 @@ setValidity("SCDDParams", function(object) {
     checks <- c(nGenes = checkInt(v$nGenes, lower = 1),
                 nCells = checkInt(v$nCells, lower = 1),
                 seed = checkInt(v$seed, lower = 0),
-                SCDat = checkClass(v$SCdat, "SummarizedExperiment"),
+                SCDat = checkClass(v$SCdat, "SingleCellExperiment"),
                 nDE = checkInt(v$nDE, lower = 0),
                 nDP = checkInt(v$nDP, lower = 0),
                 nDM = checkInt(v$nDM, lower = 0),
@@ -102,8 +102,8 @@ setMethod("show", "SCDDParams", function(object) {
     SCdat <- getParam(object, "SCdat")
     cat("Data:", "\n")
     cat("(SCdat)", "\n")
-    cat("SummarizedExperiment with", dim(SCdat)[1], "features and",
-        dim(SCdat)[2], "samples", "\n\n")
+    cat("SingleCellExperiment with", dim(SCdat)[1], "features and",
+        dim(SCdat)[2], "cells", "\n\n")
 
     showPP(object, pp)
 })

man/SCDDParams.Rd

@@ -18,7 +18,7 @@ The SCDD simulation uses the following parameters:
     \item{\code{nCells}}{The number of cells to simulate in each condition.}
     \item{\code{[seed]}}{Seed to use for generating random numbers.}
     \item{\code{SCdat}}{
-    \code{\link[SummarizedExperiment]{SummarizedExperiment}} containing real
+    \code{\link[SingleCellExperiment]{SingleCellExperiment}} containing real
     data.}
     \item{\code{nDE}}{Number of DE genes to simulate.}
     \item{\code{nDP}}{Number of DP genes to simulate.}
@@ -36,7 +36,7 @@ The SCDD simulation uses the following parameters:
 
 The parameters not shown in brackets can be estimated from real data using
 \code{\link{scDDEstimate}}. See \code{\link[scDD]{simulateSet}} for more
-details of the parameters. For details of the Splatter implementation of the
-scDD simulation see \code{\link{scDDSimulate}}.
+details about the parameters. For details of the Splatter implementation of
+the scDD simulation see \code{\link{scDDSimulate}}.
 }