From e1de64de624f60da95a8542abbd58151ac73374a Mon Sep 17 00:00:00 2001
From: Luke Zappia <lazappi@users.noreply.github.com>
Date: Thu, 7 Sep 2017 15:14:52 +1000
Subject: [PATCH] Update simulation documentation

---
 NAMESPACE                     | 24 ++++-----
 R/lun-estimate.R              | 10 ++--
 R/lun-simulate.R              | 11 ++--
 R/lun2-estimate.R             | 13 ++---
 R/lun2-simulate.R             |  8 +--
 R/scDD-estimate.R             | 12 +++--
 R/scDD-simulate.R             | 11 ++--
 R/simple-estimate.R           | 11 ++--
 R/simple-simulate.R           |  6 +--
 R/splat-estimate.R            |  9 ++--
 R/splat-simulate.R            | 97 +++++++++++++++++------------------
 man/lun2Estimate.Rd           | 11 ++--
 man/lun2Simulate.Rd           |  2 +-
 man/lunEstimate.Rd            |  8 +--
 man/lunSimulate.Rd            |  4 +-
 man/scDDEstimate.Rd           | 10 ++--
 man/scDDSimulate.Rd           |  7 +--
 man/simpleEstimate.Rd         |  9 ++--
 man/simpleSimulate.Rd         |  2 +-
 man/splatEstimate.Rd          |  9 ++--
 man/splatSimBCVMeans.Rd       |  4 +-
 man/splatSimBatchCellMeans.Rd |  4 +-
 man/splatSimBatchEffects.Rd   |  4 +-
 man/splatSimCellMeans.Rd      |  4 +-
 man/splatSimDE.Rd             |  4 +-
 man/splatSimDropout.Rd        |  4 +-
 man/splatSimGeneMeans.Rd      |  4 +-
 man/splatSimLibSizes.Rd       |  4 +-
 man/splatSimTrueCounts.Rd     |  4 +-
 man/splatSimulate.Rd          | 25 ++++-----
 30 files changed, 170 insertions(+), 165 deletions(-)

diff --git a/NAMESPACE b/NAMESPACE
index bf36ba0..53c0acc 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -1,14 +1,14 @@
 # Generated by roxygen2: do not edit by hand
 
-S3method(lun2Estimate,SCESet)
+S3method(lun2Estimate,SingleCellExperiment)
 S3method(lun2Estimate,matrix)
-S3method(lunEstimate,SCESet)
+S3method(lunEstimate,SingleCellExperiment)
 S3method(lunEstimate,matrix)
-S3method(scDDEstimate,SCESet)
+S3method(scDDEstimate,SingleCellExperiment)
 S3method(scDDEstimate,matrix)
-S3method(simpleEstimate,SCESet)
+S3method(simpleEstimate,SingleCellExperiment)
 S3method(simpleEstimate,matrix)
-S3method(splatEstimate,SCESet)
+S3method(splatEstimate,SingleCellExperiment)
 S3method(splatEstimate,matrix)
 export(addGeneLengths)
 export(compareSCESets)
@@ -46,12 +46,16 @@ exportClasses(SCDDParams)
 exportClasses(SimpleParams)
 exportClasses(SplatParams)
 importFrom(Biobase,"fData<-")
-importFrom(Biobase,"pData<-")
-importFrom(Biobase,assayData)
 importFrom(Biobase,fData)
-importFrom(Biobase,pData)
 importFrom(BiocParallel,SerialParam)
 importFrom(BiocParallel,bplapply)
+importFrom(SingleCellExperiment,SingleCellExperiment)
+importFrom(SummarizedExperiment,"assays<-")
+importFrom(SummarizedExperiment,"colData<-")
+importFrom(SummarizedExperiment,"rowData<-")
+importFrom(SummarizedExperiment,assays)
+importFrom(SummarizedExperiment,colData)
+importFrom(SummarizedExperiment,rowData)
 importFrom(checkmate,checkCharacter)
 importFrom(checkmate,checkClass)
 importFrom(checkmate,checkDataFrame)
@@ -88,10 +92,6 @@ importFrom(methods,slot)
 importFrom(methods,slotNames)
 importFrom(methods,validObject)
 importFrom(scater,"cpm<-")
-importFrom(scater,"set_exprs<-")
-importFrom(scater,counts)
-importFrom(scater,get_exprs)
-importFrom(scater,newSCESet)
 importFrom(stats,dnbinom)
 importFrom(stats,median)
 importFrom(stats,model.matrix)
diff --git a/R/lun-estimate.R b/R/lun-estimate.R
index 5cfc46b..8970079 100644
--- a/R/lun-estimate.R
+++ b/R/lun-estimate.R
@@ -2,8 +2,8 @@
 #'
 #' 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 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
@@ -24,8 +24,8 @@ lunEstimate <- function(counts, params = newLunParams()) {
 
 #' @rdname lunEstimate
 #' @export
-lunEstimate.SCESet <- function(counts, params = newLunParams()) {
-    counts <- scater::counts(counts)
+lunEstimate.SingleCellExperiment <- function(counts, params = newLunParams()) {
+    counts <- SingleCellExperiment::counts(counts)
     lunEstimate(counts, params)
 }
 
@@ -39,4 +39,4 @@ lunEstimate.matrix <- function(counts, params = newLunParams()) {
                         groupCells = ncol(counts))
 
     return(params)
-}
\ No newline at end of file
+}
diff --git a/R/lun-simulate.R b/R/lun-simulate.R
index 8ced43e..aa7337c 100644
--- a/R/lun-simulate.R
+++ b/R/lun-simulate.R
@@ -19,8 +19,8 @@
 #'
 #' See \code{\link{LunParams}} for details of the parameters.
 #'
-#' @return SCESet object containing the simulated counts and intermediate
-#' values.
+#' @return SingleCellExperiment object containing the simulated counts and
+#' intermediate values.
 #'
 #' @references
 #' Lun ATL, Bach K, Marioni JC. Pooling across cells to normalize single-cell
@@ -33,9 +33,8 @@
 #' @examples
 #' sim <- lunSimulate()
 #'
-#' @importFrom Biobase fData fData<- pData pData<-
-#' @importFrom methods new
-#' @importFrom scater newSCESet set_exprs<-
+#' @importFrom SummarizedExperiment rowData rowData<- colData colData<-
+#' @importFrom SingleCellExperiment SingleCellExperiment
 #' @importFrom stats rnorm rgamma rnbinom
 #' @export
 lunSimulate <- function(params = newLunParams(), verbose = TRUE, ...) {
@@ -110,7 +109,7 @@ lunSimulate <- function(params = newLunParams(), verbose = TRUE, ...) {
                              size = 1 / count.disp),
                      nrow = nGenes, ncol = nCells)
 
-    if (verbose) {message("Creating final SCESet...")}
+    if (verbose) {message("Creating final dataset...")}
     rownames(counts) <- gene.names
     colnames(counts) <- cell.names
 
diff --git a/R/lun2-estimate.R b/R/lun2-estimate.R
index cca9f6e..b4786b4 100644
--- a/R/lun2-estimate.R
+++ b/R/lun2-estimate.R
@@ -2,8 +2,8 @@
 #'
 #' Estimate simulation parameters for the Lun2 simulation from a real dataset.
 #'
-#' @param counts either a counts matrix or an SCESet object containing count
-#'        data to estimate parameters from.
+#' @param counts either a counts matrix or a SingleCellExperiment object
+#'        containing count data to estimate parameters from.
 #' @param plates integer vector giving the plate that each cell originated from.
 #' @param params Lun2Params object to store estimated values in.
 #' @param min.size minimum size of clusters when identifying group of cells in
@@ -36,10 +36,11 @@ lun2Estimate <- function(counts, plates, params = newLun2Params(),
 
 #' @rdname lun2Estimate
 #' @export
-lun2Estimate.SCESet <- function(counts, plates, params = newLun2Params(),
-                                min.size = 200, verbose = TRUE,
-                                BPPARAM = SerialParam()) {
-    counts <- scater::counts(counts)
+lun2Estimate.SingleCellExperiment <- function(counts, plates,
+                                              params = newLun2Params(),
+                                              min.size = 200, verbose = TRUE,
+                                              BPPARAM = SerialParam()) {
+    counts <- SingleCellExperiment::counts(counts)
     lun2Estimate(counts, plates, params, min.size = min.size, verbose = verbose)
 }
 
diff --git a/R/lun2-simulate.R b/R/lun2-simulate.R
index 439e3c6..21e3cdb 100644
--- a/R/lun2-simulate.R
+++ b/R/lun2-simulate.R
@@ -26,7 +26,7 @@
 #' number in the dataset used in the estimation step but has the downside that
 #' some genes or cells may be simulated multiple times.
 #'
-#' @return SCESet containing simulated counts.
+#' @return SingleCellExperiment containing simulated counts.
 #'
 #' @references
 #' Lun ATL, Marioni JC. Overcoming confounding plate effects in differential
@@ -39,8 +39,8 @@
 #' @examples
 #' sim <- lun2Simulate()
 #' @export
-#' @importFrom methods new
-#' @importFrom scater newSCESet set_exprs<-
+#' @importFrom SummarizedExperiment assays<-
+#' @importFrom SingleCellExperiment SingleCellExperiment
 lun2Simulate <- function(params = newLun2Params(), zinb = FALSE,
                          verbose = TRUE, ...) {
 
@@ -167,7 +167,7 @@ lun2Simulate <- function(params = newLun2Params(), zinb = FALSE,
         counts[is.zero] <- 0
     }
 
-    if (verbose) {message("Creating final SCESet...")}
+    if (verbose) {message("Creating final dataset...")}
 
     rownames(cells) <- cell.names
     rownames(features) <- gene.names
diff --git a/R/scDD-estimate.R b/R/scDD-estimate.R
index f1aba9c..5f52157 100644
--- a/R/scDD-estimate.R
+++ b/R/scDD-estimate.R
@@ -2,8 +2,8 @@
 #'
 #' Estimate simulation parameters for the scDD simulation from a real dataset.
 #'
-#' @param counts either a counts matrix or an SCESet object containing count
-#'        data to estimate parameters from.
+#' @param counts either a counts matrix or a SingleCellExperiment object
+#'        containing count data to estimate parameters from.
 #' @param conditions Vector giving the condition that each cell belongs to.
 #'        Conditions can be 1 or 2.
 #' @param params SCDDParams object to store estimated values in.
@@ -36,9 +36,11 @@ scDDEstimate <- function(counts, conditions, params = newSCDDParams(),
 
 #' @rdname scDDEstimate
 #' @export
-scDDEstimate.SCESet <- function(counts, conditions, params = newSCDDParams(),
-                                verbose = TRUE, BPPARAM = SerialParam()) {
-    counts <- scater::counts(counts)
+scDDEstimate.SingleCellExperiment <- function(counts, conditions,
+                                              params = newSCDDParams(),
+                                              verbose = TRUE,
+                                              BPPARAM = SerialParam()) {
+    counts <- SingleCellExperiment::counts(counts)
     scDDEstimate(counts, conditions, params, verbose, BPPARAM)
 }
 
diff --git a/R/scDD-simulate.R b/R/scDD-simulate.R
index b3d9498..704e14a 100644
--- a/R/scDD-simulate.R
+++ b/R/scDD-simulate.R
@@ -16,10 +16,11 @@
 #' @details
 #' This function is just a wrapper around \code{\link[scDD]{simulateSet}} that
 #' takes a \code{\link{SCDDParams}}, runs the simulation then converts the
-#' output to an \code{\link[scater]{SCESet}} object. See
-#' \code{\link[scDD]{simulateSet}} for more details of how the simulation works.
+#' output to a \code{\link[SingleCellExperiment]{SingleCellExperiment}} object.
+#' See \code{\link[scDD]{simulateSet}} for more details about how the simulation
+#' works.
 #'
-#' @return SCESet containing simulated counts
+#' @return SingleCellExperiment containing simulated counts
 #'
 #' @references
 #' Korthauer KD, Chu L-F, Newton MA, Li Y, Thomson J, Stewart R, et al. A
@@ -35,8 +36,8 @@
 #' sim <- scDDSimulate()
 #' }
 #' @export
-#' @importFrom scater newSCESet
 #' @importFrom BiocParallel SerialParam
+#' @importFrom SingleCellExperiment SingleCellExperiment
 scDDSimulate <- function(params = newSCDDParams(), plots = FALSE,
                          plot.file = NULL, verbose = TRUE,
                          BPPARAM = SerialParam(), ...) {
@@ -94,7 +95,7 @@ scDDSimulate <- function(params = newSCDDParams(), plots = FALSE,
     foldchanges <- scDD.sim[[2]]
     de.status <- rownames(counts)
 
-    if (verbose) {message("Creating SCESet...")}
+    if (verbose) {message("Creating final dataset...")}
     cell.names <- paste0("Cell", seq_len(nCells * 2))
     gene.names <- paste0("Gene", seq_len(getParam(params, "nGenes")))
 
diff --git a/R/simple-estimate.R b/R/simple-estimate.R
index 1225bec..793be3c 100644
--- a/R/simple-estimate.R
+++ b/R/simple-estimate.R
@@ -2,8 +2,8 @@
 #'
 #' Estimate simulation parameters for the simple simulation from a real dataset.
 #'
-#' @param counts either a counts matrix or an SCESet object containing count
-#'        data to estimate parameters from.
+#' @param counts either a counts matrix or a SingleCellExperiment object
+#'        containing count data to estimate parameters from.
 #' @param params SimpleParams object to store estimated values in.
 #'
 #' @details
@@ -26,8 +26,9 @@ simpleEstimate <- function(counts, params = newSimpleParams()) {
 
 #' @rdname simpleEstimate
 #' @export
-simpleEstimate.SCESet <- function(counts, params = newSimpleParams()) {
-    counts <- scater::counts(counts)
+simpleEstimate.SingleCellExperiment <- function(counts,
+                                                params = newSimpleParams()) {
+    counts <- SingleCellExperiment::counts(counts)
     simpleEstimate(counts, params)
 }
 
@@ -53,4 +54,4 @@ simpleEstimate.matrix <- function(counts, params = newSimpleParams()) {
                         mean.rate = unname(means.fit$estimate["rate"]))
 
     return(params)
-}
\ No newline at end of file
+}
diff --git a/R/simple-simulate.R b/R/simple-simulate.R
index add6825..3c074ce 100644
--- a/R/simple-simulate.R
+++ b/R/simple-simulate.R
@@ -15,14 +15,14 @@
 #' \code{size = 1 / counts.disp}. See \code{\link{SimpleParams}} for more
 #' details of the parameters.
 #'
-#' @return SCESet containing simulated counts
+#' @return SingleCellExperiment containing simulated counts
 #' @examples
 #' sim <- simpleSimulate()
 #' # Override default parameters
 #' sim <- simpleSimulate(nGenes = 1000, nCells = 50)
 #' @export
 #' @importFrom stats rgamma rnbinom
-#' @importFrom scater newSCESet
+#' @importFrom SingleCellExperiment SingleCellExperiment
 simpleSimulate <- function(params = newSimpleParams(), verbose = TRUE, ...) {
 
     checkmate::assertClass(params, "SimpleParams")
@@ -47,7 +47,7 @@ simpleSimulate <- function(params = newSimpleParams(), verbose = TRUE, ...) {
                              size = 1 / count.disp),
                      nrow = nGenes, ncol = nCells)
 
-    if (verbose) {message("Creating final SCESet...")}
+    if (verbose) {message("Creating final dataset...")}
     cell.names <- paste0("Cell", seq_len(nCells))
     gene.names <- paste0("Gene", seq_len(nGenes))
 
diff --git a/R/splat-estimate.R b/R/splat-estimate.R
index 0c2b036..b1523f2 100644
--- a/R/splat-estimate.R
+++ b/R/splat-estimate.R
@@ -4,8 +4,8 @@
 #' dataset. See the individual estimation functions for more details on how this
 #' is done.
 #'
-#' @param counts either a counts matrix or an SCESet object containing count
-#'        data to estimate parameters from.
+#' @param counts either a counts matrix or a SingleCellExperiment object
+#'        containing count data to estimate parameters from.
 #' @param params SplatParams object to store estimated values in.
 #'
 #' @seealso
@@ -26,8 +26,9 @@ splatEstimate <- function(counts, params = newSplatParams()) {
 
 #' @rdname splatEstimate
 #' @export
-splatEstimate.SCESet <- function(counts, params = newSplatParams()) {
-    counts <- scater::counts(counts)
+splatEstimate.SingleCellExperiment <- function(counts,
+                                               params = newSplatParams()) {
+    counts <- SingleCellExperiment::counts(counts)
     splatEstimate(counts, params)
 }
 
diff --git a/R/splat-simulate.R b/R/splat-simulate.R
index 7967e70..38bbf7d 100644
--- a/R/splat-simulate.R
+++ b/R/splat-simulate.R
@@ -31,15 +31,16 @@
 #'     \item Simulate BCV adjusted cell means
 #'     \item Simulate true counts
 #'     \item Simulate dropout
-#'     \item Create final SCESet object
+#'     \item Create final dataset
 #' }
 #'
-#' The final output is an \code{\link[scater]{SCESet}} object that contains the
-#' simulated counts but also the values for various intermediate steps. These
-#' are stored in the \code{\link[Biobase]{phenoData}} (for cell specific
-#' information), \code{\link[Biobase]{featureData}} (for gene specific
-#' information) or \code{\link[Biobase]{assayData}} (for gene by cell matrices)
-#' slots. This additional information includes:
+#' The final output is a
+#' \code{\link[SingleCellExperiment]{SingleCellExperiment}} object that
+#' contains the simulated counts but also the values for various intermediate
+#' steps. These are stored in the \code{\link[SummarizedExperiment]{colData}}
+#' (for cell specific information), \code{\link[SummarizedExperiment]{rowData}}
+#' (for gene specific information) or \code{\link[SummarizedExperiment]{assays}}
+#' (for gene by cell matrices) slots. This additional information includes:
 #' \describe{
 #'     \item{\code{phenoData}}{
 #'         \describe{
@@ -83,12 +84,12 @@
 #'     }
 #' }
 #'
-#' Values that have been added by Splatter are named using \code{CamelCase} in
-#' order to differentiate them from the values added by Scater which uses
-#' \code{underscore_naming}.
+#' Values that have been added by Splatter are named using \code{UpperCamelCase}
+#' in order to differentiate them from the values added by analysis packages
+#' which typically use \code{underscore_naming}.
 #'
-#' @return SCESet object containing the simulated counts and intermediate
-#' values.
+#' @return SingleCellExperiment object containing the simulated counts and
+#' intermediate values.
 #'
 #' @seealso
 #' \code{\link{splatSimLibSizes}}, \code{\link{splatSimGeneMeans}},
@@ -113,9 +114,9 @@
 #' # Simulate paths
 #' sim <- splatSimulate(method = "paths")
 #' }
-#' @importFrom Biobase fData pData pData<- assayData
+#' @importFrom SummarizedExperiment rowData colData colData<- assays
+#' @importFrom SingleCellExperiment SingleCellExperiment
 #' @importFrom methods validObject
-#' @importFrom scater newSCESet counts set_exprs<- get_exprs
 #' @export
 splatSimulate <- function(params = newSplatParams(),
                           method = c("single", "groups", "paths"),
@@ -158,7 +159,7 @@ splatSimulate <- function(params = newSplatParams(),
         group.names <- paste0("Path", seq_len(nGroups))
     }
 
-    # Create SCESet with dummy counts to store simulation
+    # Create SingleCellExperiment to store simulation
     cells <-  data.frame(Cell = cell.names)
     rownames(cells) <- cell.names
     features <- data.frame(Gene = gene.names)
@@ -242,12 +243,12 @@ splatSimulatePaths <- function(params = newSplatParams(), verbose = TRUE, ...) {
 #'
 #' Simulate expected library sizes from a log-normal distribution
 #'
-#' @param sim SCESet to add library size to.
+#' @param sim SingleCellExperiment to add library size to.
 #' @param params SplatParams object with simulation parameters.
 #'
-#' @return SCESet with simulated library sizes.
+#' @return SingleCellExperiment with simulated library sizes.
 #'
-#' @importFrom Biobase pData pData<-
+#' @importFrom SummarizedExperiment colData colData<-
 #' @importFrom stats rlnorm
 splatSimLibSizes <- function(sim, params) {
 
@@ -267,12 +268,12 @@ splatSimLibSizes <- function(sim, params) {
 #' expression factors. Genes with an outlier factor not equal to 1 are replaced
 #' with the median mean expression multiplied by the outlier factor.
 #'
-#' @param sim SCESet to add gene means to.
+#' @param sim SingleCellExperiment to add gene means to.
 #' @param params SplatParams object with simulation parameters.
 #'
-#' @return SCESet with simulated gene means.
+#' @return SingleCellExperiment with simulated gene means.
 #'
-#' @importFrom Biobase fData fData<-
+#' @importFrom SummarizedExperiment rowData rowData<-
 #' @importFrom stats rgamma median
 splatSimGeneMeans <- function(sim, params) {
 
@@ -308,12 +309,12 @@ splatSimGeneMeans <- function(sim, params) {
 #' using \code{\link{getLNormFactors}} and these are added along with updated
 #' means for each batch.
 #'
-#' @param sim SCESet to add batch effects to.
+#' @param sim SingleCellExperiment to add batch effects to.
 #' @param params SplatParams object with simulation parameters.
 #'
-#' @return SCESet with simulated batch effects.
+#' @return SingleCellExperiment with simulated batch effects.
 #'
-#' @importFrom Biobase fData fData<-
+#' @importFrom SummarizedExperiment rowData rowData<-
 splatSimBatchEffects <- function(sim, params) {
 
     nGenes <- getParam(params, "nGenes")
@@ -337,12 +338,12 @@ splatSimBatchEffects <- function(sim, params) {
 #' Simulate a mean for each gene in each cell incorporating batch effect
 #' factors.
 #'
-#' @param sim SCESet to add batch means to.
+#' @param sim SingleCellExperiment to add batch means to.
 #' @param params SplatParams object with simulation parameters.
 #'
-#' @return SCESet with simulated batch means.
+#' @return SingleCellExperiment with simulated batch means.
 #'
-#' @importFrom Biobase fData fData<-
+#' @importFrom SummarizedExperiment rowData rowData<-
 splatSimBatchCellMeans <- function(sim, params) {
 
     nBatches <- getParam(params, "nBatches")
@@ -380,16 +381,16 @@ splatSimBatchCellMeans <- function(sim, params) {
 #' along with updated means for each group. For paths care is taked to make sure
 #' they are simulated in the correct order.
 #'
-#' @param sim SCESet to add differential expression to.
+#' @param sim SingleCellExperiment to add differential expression to.
 #' @param params splatParams object with simulation parameters.
 #'
-#' @return SCESet with simulated differential expression.
+#' @return SingleCellExperiment with simulated differential expression.
 #'
 #' @name splatSimDE
 NULL
 
 #' @rdname splatSimDE
-#' @importFrom Biobase fData
+#' @importFrom SummarizedExperiment rowData
 splatSimGroupDE <- function(sim, params) {
 
     nGenes <- getParam(params, "nGenes")
@@ -411,7 +412,7 @@ splatSimGroupDE <- function(sim, params) {
 }
 
 #' @rdname splatSimDE
-#' @importFrom Biobase fData
+#' @importFrom SummarizedExperiment rowData
 splatSimPathDE <- function(sim, params) {
 
     nGenes <- getParam(params, "nGenes")
@@ -446,17 +447,16 @@ splatSimPathDE <- function(sim, params) {
 #' random position on the appropriate path (when simulating paths). The selected
 #' means are adjusted for each cell's expected library size.
 #'
-#' @param sim SCESet to add cell means to.
+#' @param sim SingleCellExperiment to add cell means to.
 #' @param params SplatParams object with simulation parameters.
 #'
-#' @return SCESet with added cell means.
+#' @return SingleCellExperiment with added cell means.
 #'
 #' @name splatSimCellMeans
 NULL
 
 #' @rdname splatSimCellMeans
-#' @importFrom Biobase fData pData
-#' @importFrom scater set_exprs<- get_exprs
+#' @importFrom SummarizedExperiment rowData colData assays assays<-
 splatSimSingleCellMeans <- function(sim, params) {
 
     nCells <- getParam(params, "nCells")
@@ -477,8 +477,7 @@ splatSimSingleCellMeans <- function(sim, params) {
 }
 
 #' @rdname splatSimCellMeans
-#' @importFrom Biobase fData pData
-#' @importFrom scater get_exprs set_exprs<-
+#' @importFrom SummarizedExperiment rowData colData assays assays<-
 splatSimGroupCellMeans <- function(sim, params) {
 
     nGroups <- getParam(params, "nGroups")
@@ -503,8 +502,7 @@ splatSimGroupCellMeans <- function(sim, params) {
 }
 
 #' @rdname splatSimCellMeans
-#' @importFrom Biobase fData pData
-#' @importFrom scater set_exprs<-
+#' @importFrom SummarizedExperiment rowData colData colData<- assays assays<-
 #' @importFrom stats rbinom
 splatSimPathCellMeans <- function(sim, params) {
 
@@ -605,13 +603,12 @@ splatSimPathCellMeans <- function(sim, params) {
 #' mean-variance trend using Biological Coefficient of Variation taken from
 #' and inverse gamma distribution.
 #'
-#' @param sim SCESet to add BCV means to.
+#' @param sim SingleCellExperiment to add BCV means to.
 #' @param params SplatParams object with simulation parameters.
 #'
-#' @return SCESet with simulated BCV means.
+#' @return SingleCellExperiment with simulated BCV means.
 #'
-#' @importFrom Biobase fData pData
-#' @importFrom scater get_exprs set_exprs<-
+#' @importFrom SummarizedExperiment rowData colData assays assays<-
 #' @importFrom stats rchisq rgamma
 splatSimBCVMeans <- function(sim, params) {
 
@@ -650,13 +647,12 @@ splatSimBCVMeans <- function(sim, params) {
 #' distribution where Each gene in each cell has it's own mean based on the
 #' group (or path position), expected library size and BCV.
 #'
-#' @param sim SCESet to add true counts to.
+#' @param sim SingleCellExperiment to add true counts to.
 #' @param params SplatParams object with simulation parameters.
 #'
-#' @return SCESet with simulated true counts.
+#' @return SingleCellExperiment with simulated true counts.
 #'
-#' @importFrom Biobase fData pData
-#' @importFrom scater get_exprs set_exprs<-
+#' @importFrom SummarizedExperiment rowData colData assays assays<-
 #' @importFrom stats rpois
 splatSimTrueCounts <- function(sim, params) {
 
@@ -684,13 +680,12 @@ splatSimTrueCounts <- function(sim, params) {
 #' gene in each cell. These probabilities are used in a Bernoulli distribution
 #' to decide which counts should be dropped.
 #'
-#' @param sim SCESet to add dropout to.
+#' @param sim SingleCellExperiment to add dropout to.
 #' @param params SplatParams object with simulation parameters.
 #'
-#' @return SCESet with simulated dropout and observed counts.
+#' @return SingleCellExperiment with simulated dropout and observed counts.
 #'
-#' @importFrom Biobase fData pData
-#' @importFrom scater get_exprs set_exprs<-
+#' @importFrom SummarizedExperiment rowData colData assays assays<-
 #' @importFrom stats rbinom
 splatSimDropout <- function(sim, params) {
 
diff --git a/man/lun2Estimate.Rd b/man/lun2Estimate.Rd
index 3696347..d0e240e 100644
--- a/man/lun2Estimate.Rd
+++ b/man/lun2Estimate.Rd
@@ -2,22 +2,23 @@
 % Please edit documentation in R/lun2-estimate.R
 \name{lun2Estimate}
 \alias{lun2Estimate}
-\alias{lun2Estimate.SCESet}
+\alias{lun2Estimate.SingleCellExperiment}
 \alias{lun2Estimate.matrix}
 \title{Estimate Lun2 simulation parameters}
 \usage{
 lun2Estimate(counts, plates, params = newLun2Params(), min.size = 200,
   verbose = TRUE, BPPARAM = SerialParam())
 
-\method{lun2Estimate}{SCESet}(counts, plates, params = newLun2Params(),
-  min.size = 200, verbose = TRUE, BPPARAM = SerialParam())
+\method{lun2Estimate}{SingleCellExperiment}(counts, plates,
+  params = newLun2Params(), min.size = 200, verbose = TRUE,
+  BPPARAM = SerialParam())
 
 \method{lun2Estimate}{matrix}(counts, plates, params = newLun2Params(),
   min.size = 200, verbose = TRUE, BPPARAM = SerialParam())
 }
 \arguments{
-\item{counts}{either a counts matrix or an SCESet object containing count
-data to estimate parameters from.}
+\item{counts}{either a counts matrix or a SingleCellExperiment object
+containing count data to estimate parameters from.}
 
 \item{plates}{integer vector giving the plate that each cell originated from.}
 
diff --git a/man/lun2Simulate.Rd b/man/lun2Simulate.Rd
index 491ba67..e091ce9 100644
--- a/man/lun2Simulate.Rd
+++ b/man/lun2Simulate.Rd
@@ -17,7 +17,7 @@ lun2Simulate(params = newLun2Params(), zinb = FALSE, verbose = TRUE, ...)
 \code{params}.}
 }
 \value{
-SCESet containing simulated counts.
+SingleCellExperiment containing simulated counts.
 }
 \description{
 Simulate single-cell RNA-seq count data using the method described in Lun
diff --git a/man/lunEstimate.Rd b/man/lunEstimate.Rd
index 8ee55be..82f5e67 100644
--- a/man/lunEstimate.Rd
+++ b/man/lunEstimate.Rd
@@ -2,19 +2,19 @@
 % Please edit documentation in R/lun-estimate.R
 \name{lunEstimate}
 \alias{lunEstimate}
-\alias{lunEstimate.SCESet}
+\alias{lunEstimate.SingleCellExperiment}
 \alias{lunEstimate.matrix}
 \title{Estimate Lun simulation parameters}
 \usage{
 lunEstimate(counts, params = newLunParams())
 
-\method{lunEstimate}{SCESet}(counts, params = newLunParams())
+\method{lunEstimate}{SingleCellExperiment}(counts, params = newLunParams())
 
 \method{lunEstimate}{matrix}(counts, params = newLunParams())
 }
 \arguments{
-\item{counts}{either a counts matrix or an SCESet object containing count
-data to estimate parameters from.}
+\item{counts}{either a counts matrix or an SingleCellExperiment object
+containing count data to estimate parameters from.}
 
 \item{params}{LunParams object to store estimated values in.}
 }
diff --git a/man/lunSimulate.Rd b/man/lunSimulate.Rd
index 4ccd94a..0e48781 100644
--- a/man/lunSimulate.Rd
+++ b/man/lunSimulate.Rd
@@ -15,8 +15,8 @@ lunSimulate(params = newLunParams(), verbose = TRUE, ...)
 \code{params}.}
 }
 \value{
-SCESet object containing the simulated counts and intermediate
-values.
+SingleCellExperiment object containing the simulated counts and
+intermediate values.
 }
 \description{
 Simulate single-cell RNA-seq count data using the method described in Lun,
diff --git a/man/scDDEstimate.Rd b/man/scDDEstimate.Rd
index 44bd401..6eb052e 100644
--- a/man/scDDEstimate.Rd
+++ b/man/scDDEstimate.Rd
@@ -2,22 +2,22 @@
 % Please edit documentation in R/scDD-estimate.R
 \name{scDDEstimate}
 \alias{scDDEstimate}
-\alias{scDDEstimate.SCESet}
+\alias{scDDEstimate.SingleCellExperiment}
 \alias{scDDEstimate.matrix}
 \title{Estimate scDD simulation parameters}
 \usage{
 scDDEstimate(counts, conditions, params = newSCDDParams(), verbose = TRUE,
   BPPARAM = SerialParam())
 
-\method{scDDEstimate}{SCESet}(counts, conditions, params = newSCDDParams(),
-  verbose = TRUE, BPPARAM = SerialParam())
+\method{scDDEstimate}{SingleCellExperiment}(counts, conditions,
+  params = newSCDDParams(), verbose = TRUE, BPPARAM = SerialParam())
 
 \method{scDDEstimate}{matrix}(counts, conditions, params = newSCDDParams(),
   verbose = TRUE, BPPARAM = SerialParam())
 }
 \arguments{
-\item{counts}{either a counts matrix or an SCESet object containing count
-data to estimate parameters from.}
+\item{counts}{either a counts matrix or a SingleCellExperiment object
+containing count data to estimate parameters from.}
 
 \item{conditions}{Vector giving the condition that each cell belongs to.
 Conditions can be 1 or 2.}
diff --git a/man/scDDSimulate.Rd b/man/scDDSimulate.Rd
index 387413b..24f4c5a 100644
--- a/man/scDDSimulate.Rd
+++ b/man/scDDSimulate.Rd
@@ -25,7 +25,7 @@ giving the parallel back-end to be used. Default is
 \code{params}.}
 }
 \value{
-SCESet containing simulated counts
+SingleCellExperiment containing simulated counts
 }
 \description{
 Simulate counts using the scDD method.
@@ -33,8 +33,9 @@ Simulate counts using the scDD method.
 \details{
 This function is just a wrapper around \code{\link[scDD]{simulateSet}} that
 takes a \code{\link{SCDDParams}}, runs the simulation then converts the
-output to an \code{\link[scater]{SCESet}} object. See
-\code{\link[scDD]{simulateSet}} for more details of how the simulation works.
+output to a \code{\link[SingleCellExperiment]{SingleCellExperiment}} object.
+See \code{\link[scDD]{simulateSet}} for more details about how the simulation
+works.
 }
 \examples{
 \dontrun{
diff --git a/man/simpleEstimate.Rd b/man/simpleEstimate.Rd
index 3be8654..159c879 100644
--- a/man/simpleEstimate.Rd
+++ b/man/simpleEstimate.Rd
@@ -2,19 +2,20 @@
 % Please edit documentation in R/simple-estimate.R
 \name{simpleEstimate}
 \alias{simpleEstimate}
-\alias{simpleEstimate.SCESet}
+\alias{simpleEstimate.SingleCellExperiment}
 \alias{simpleEstimate.matrix}
 \title{Estimate simple simulation parameters}
 \usage{
 simpleEstimate(counts, params = newSimpleParams())
 
-\method{simpleEstimate}{SCESet}(counts, params = newSimpleParams())
+\method{simpleEstimate}{SingleCellExperiment}(counts,
+  params = newSimpleParams())
 
 \method{simpleEstimate}{matrix}(counts, params = newSimpleParams())
 }
 \arguments{
-\item{counts}{either a counts matrix or an SCESet object containing count
-data to estimate parameters from.}
+\item{counts}{either a counts matrix or a SingleCellExperiment object
+containing count data to estimate parameters from.}
 
 \item{params}{SimpleParams object to store estimated values in.}
 }
diff --git a/man/simpleSimulate.Rd b/man/simpleSimulate.Rd
index b2f5fda..e52be18 100644
--- a/man/simpleSimulate.Rd
+++ b/man/simpleSimulate.Rd
@@ -15,7 +15,7 @@ simpleSimulate(params = newSimpleParams(), verbose = TRUE, ...)
 \code{params}.}
 }
 \value{
-SCESet containing simulated counts
+SingleCellExperiment containing simulated counts
 }
 \description{
 Simulate counts from a simple negative binomial distribution without
diff --git a/man/splatEstimate.Rd b/man/splatEstimate.Rd
index f698fd9..b14d519 100644
--- a/man/splatEstimate.Rd
+++ b/man/splatEstimate.Rd
@@ -2,19 +2,20 @@
 % Please edit documentation in R/splat-estimate.R
 \name{splatEstimate}
 \alias{splatEstimate}
-\alias{splatEstimate.SCESet}
+\alias{splatEstimate.SingleCellExperiment}
 \alias{splatEstimate.matrix}
 \title{Estimate Splat simulation parameters}
 \usage{
 splatEstimate(counts, params = newSplatParams())
 
-\method{splatEstimate}{SCESet}(counts, params = newSplatParams())
+\method{splatEstimate}{SingleCellExperiment}(counts,
+  params = newSplatParams())
 
 \method{splatEstimate}{matrix}(counts, params = newSplatParams())
 }
 \arguments{
-\item{counts}{either a counts matrix or an SCESet object containing count
-data to estimate parameters from.}
+\item{counts}{either a counts matrix or a SingleCellExperiment object
+containing count data to estimate parameters from.}
 
 \item{params}{SplatParams object to store estimated values in.}
 }
diff --git a/man/splatSimBCVMeans.Rd b/man/splatSimBCVMeans.Rd
index 315b5ae..9ffc622 100644
--- a/man/splatSimBCVMeans.Rd
+++ b/man/splatSimBCVMeans.Rd
@@ -7,12 +7,12 @@
 splatSimBCVMeans(sim, params)
 }
 \arguments{
-\item{sim}{SCESet to add BCV means to.}
+\item{sim}{SingleCellExperiment to add BCV means to.}
 
 \item{params}{SplatParams object with simulation parameters.}
 }
 \value{
-SCESet with simulated BCV means.
+SingleCellExperiment with simulated BCV means.
 }
 \description{
 Simulate means for each gene in each cell that are adjusted to follow a
diff --git a/man/splatSimBatchCellMeans.Rd b/man/splatSimBatchCellMeans.Rd
index edd0736..e0d7869 100644
--- a/man/splatSimBatchCellMeans.Rd
+++ b/man/splatSimBatchCellMeans.Rd
@@ -7,12 +7,12 @@
 splatSimBatchCellMeans(sim, params)
 }
 \arguments{
-\item{sim}{SCESet to add batch means to.}
+\item{sim}{SingleCellExperiment to add batch means to.}
 
 \item{params}{SplatParams object with simulation parameters.}
 }
 \value{
-SCESet with simulated batch means.
+SingleCellExperiment with simulated batch means.
 }
 \description{
 Simulate a mean for each gene in each cell incorporating batch effect
diff --git a/man/splatSimBatchEffects.Rd b/man/splatSimBatchEffects.Rd
index 76c4304..c047ab4 100644
--- a/man/splatSimBatchEffects.Rd
+++ b/man/splatSimBatchEffects.Rd
@@ -7,12 +7,12 @@
 splatSimBatchEffects(sim, params)
 }
 \arguments{
-\item{sim}{SCESet to add batch effects to.}
+\item{sim}{SingleCellExperiment to add batch effects to.}
 
 \item{params}{SplatParams object with simulation parameters.}
 }
 \value{
-SCESet with simulated batch effects.
+SingleCellExperiment with simulated batch effects.
 }
 \description{
 Simulate batch effects. Batch effect factors for each batch are produced
diff --git a/man/splatSimCellMeans.Rd b/man/splatSimCellMeans.Rd
index 436fd6f..de5222b 100644
--- a/man/splatSimCellMeans.Rd
+++ b/man/splatSimCellMeans.Rd
@@ -14,12 +14,12 @@ splatSimGroupCellMeans(sim, params)
 splatSimPathCellMeans(sim, params)
 }
 \arguments{
-\item{sim}{SCESet to add cell means to.}
+\item{sim}{SingleCellExperiment to add cell means to.}
 
 \item{params}{SplatParams object with simulation parameters.}
 }
 \value{
-SCESet with added cell means.
+SingleCellExperiment with added cell means.
 }
 \description{
 Simulate a gene by cell matrix giving the mean expression for each gene in
diff --git a/man/splatSimDE.Rd b/man/splatSimDE.Rd
index 85f7680..257fb1c 100644
--- a/man/splatSimDE.Rd
+++ b/man/splatSimDE.Rd
@@ -11,12 +11,12 @@ splatSimGroupDE(sim, params)
 splatSimPathDE(sim, params)
 }
 \arguments{
-\item{sim}{SCESet to add differential expression to.}
+\item{sim}{SingleCellExperiment to add differential expression to.}
 
 \item{params}{splatParams object with simulation parameters.}
 }
 \value{
-SCESet with simulated differential expression.
+SingleCellExperiment with simulated differential expression.
 }
 \description{
 Simulate differential expression. Differential expression factors for each
diff --git a/man/splatSimDropout.Rd b/man/splatSimDropout.Rd
index 166336c..7f68ba3 100644
--- a/man/splatSimDropout.Rd
+++ b/man/splatSimDropout.Rd
@@ -7,12 +7,12 @@
 splatSimDropout(sim, params)
 }
 \arguments{
-\item{sim}{SCESet to add dropout to.}
+\item{sim}{SingleCellExperiment to add dropout to.}
 
 \item{params}{SplatParams object with simulation parameters.}
 }
 \value{
-SCESet with simulated dropout and observed counts.
+SingleCellExperiment with simulated dropout and observed counts.
 }
 \description{
 A logistic function is used to form a relationshop between the expression
diff --git a/man/splatSimGeneMeans.Rd b/man/splatSimGeneMeans.Rd
index 7d738db..4a13269 100644
--- a/man/splatSimGeneMeans.Rd
+++ b/man/splatSimGeneMeans.Rd
@@ -7,12 +7,12 @@
 splatSimGeneMeans(sim, params)
 }
 \arguments{
-\item{sim}{SCESet to add gene means to.}
+\item{sim}{SingleCellExperiment to add gene means to.}
 
 \item{params}{SplatParams object with simulation parameters.}
 }
 \value{
-SCESet with simulated gene means.
+SingleCellExperiment with simulated gene means.
 }
 \description{
 Simulate gene means from a gamma distribution. Also simulates outlier
diff --git a/man/splatSimLibSizes.Rd b/man/splatSimLibSizes.Rd
index 4785021..3c5c380 100644
--- a/man/splatSimLibSizes.Rd
+++ b/man/splatSimLibSizes.Rd
@@ -7,12 +7,12 @@
 splatSimLibSizes(sim, params)
 }
 \arguments{
-\item{sim}{SCESet to add library size to.}
+\item{sim}{SingleCellExperiment to add library size to.}
 
 \item{params}{SplatParams object with simulation parameters.}
 }
 \value{
-SCESet with simulated library sizes.
+SingleCellExperiment with simulated library sizes.
 }
 \description{
 Simulate expected library sizes from a log-normal distribution
diff --git a/man/splatSimTrueCounts.Rd b/man/splatSimTrueCounts.Rd
index 4fc2464..cb2ba30 100644
--- a/man/splatSimTrueCounts.Rd
+++ b/man/splatSimTrueCounts.Rd
@@ -7,12 +7,12 @@
 splatSimTrueCounts(sim, params)
 }
 \arguments{
-\item{sim}{SCESet to add true counts to.}
+\item{sim}{SingleCellExperiment to add true counts to.}
 
 \item{params}{SplatParams object with simulation parameters.}
 }
 \value{
-SCESet with simulated true counts.
+SingleCellExperiment with simulated true counts.
 }
 \description{
 Simulate a true counts matrix. Counts are simulated from a poisson
diff --git a/man/splatSimulate.Rd b/man/splatSimulate.Rd
index d827f16..0db1f72 100644
--- a/man/splatSimulate.Rd
+++ b/man/splatSimulate.Rd
@@ -31,8 +31,8 @@ trajectories (eg. differentiation processes).}
 \code{params}.}
 }
 \value{
-SCESet object containing the simulated counts and intermediate
-values.
+SingleCellExperiment object containing the simulated counts and
+intermediate values.
 }
 \description{
 Simulate count data from a fictional single-cell RNA-seq experiment using
@@ -56,15 +56,16 @@ The simulation involves the following steps:
     \item Simulate BCV adjusted cell means
     \item Simulate true counts
     \item Simulate dropout
-    \item Create final SCESet object
+    \item Create final dataset
 }
 
-The final output is an \code{\link[scater]{SCESet}} object that contains the
-simulated counts but also the values for various intermediate steps. These
-are stored in the \code{\link[Biobase]{phenoData}} (for cell specific
-information), \code{\link[Biobase]{featureData}} (for gene specific
-information) or \code{\link[Biobase]{assayData}} (for gene by cell matrices)
-slots. This additional information includes:
+The final output is a
+\code{\link[SingleCellExperiment]{SingleCellExperiment}} object that
+contains the simulated counts but also the values for various intermediate
+steps. These are stored in the \code{\link[SummarizedExperiment]{colData}}
+(for cell specific information), \code{\link[SummarizedExperiment]{rowData}}
+(for gene specific information) or \code{\link[SummarizedExperiment]{assays}}
+(for gene by cell matrices) slots. This additional information includes:
 \describe{
     \item{\code{phenoData}}{
         \describe{
@@ -108,9 +109,9 @@ slots. This additional information includes:
     }
 }
 
-Values that have been added by Splatter are named using \code{CamelCase} in
-order to differentiate them from the values added by Scater which uses
-\code{underscore_naming}.
+Values that have been added by Splatter are named using \code{UpperCamelCase}
+in order to differentiate them from the values added by analysis packages
+which typically use \code{underscore_naming}.
 }
 \examples{
 # Simulation with default parameters
-- 
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