diff --git a/R/AllClasses.R b/R/AllClasses.R index 59432fe5ebe17e623cf3c367bacb33cdd1394b6d..36fe0b311b765b47b6d617e2ee328af9c8eb2ad4 100644 --- a/R/AllClasses.R +++ b/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, diff --git a/R/SCDDParams-methods.R b/R/SCDDParams-methods.R index 09aa786a36852cf62acdc979ca8d3e5cc9d5fb23..22c6ac198a2db3c8fab3ee445b543227fb209a4b 100644 --- a/R/SCDDParams-methods.R +++ b/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) }) diff --git a/man/SCDDParams.Rd b/man/SCDDParams.Rd index aef9df97deb3ea7b3d8625a55cf1fa51e044cc1f..894530c483b0f5685740de994b226019422d0c38 100644 --- a/man/SCDDParams.Rd +++ b/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}}. }