From 31fb64a36d112acee42a63cce9e7d2575c4666e4 Mon Sep 17 00:00:00 2001
From: Luke Zappia <lazappi@users.noreply.github.com>
Date: Fri, 29 Sep 2017 14:43:41 +1000
Subject: [PATCH] Update SCDDParams
---
R/AllClasses.R | 8 ++++----
R/SCDDParams-methods.R | 6 +++---
man/SCDDParams.Rd | 6 +++---
3 files changed, 10 insertions(+), 10 deletions(-)
diff --git a/R/AllClasses.R b/R/AllClasses.R
index 59432fe..36fe0b3 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 09aa786..22c6ac1 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 aef9df9..894530c 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}}.
}
--
GitLab