Remove references to SCESets

NAMESPACE

 # Generated by roxygen2: do not edit by hand
 
-S3method(BASiCSEstimate,SCESet)
+S3method(BASiCSEstimate,SingleCellExperiment)
 S3method(BASiCSEstimate,matrix)
 S3method(lun2Estimate,SingleCellExperiment)
 S3method(lun2Estimate,matrix)

R/BASiCS-estimate.R

@@ -2,8 +2,8 @@
 #'
 #' Estimate simulation parameters for the BASiCS 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 spike.info data.frame describing spike-ins with two columns: "Name"
 #'        giving the names of the spike-in features (must match
 #'        \code{rownames(counts)}) and "Input" giving the number of input
@@ -52,10 +52,12 @@ BASiCSEstimate <- function(counts, spike.info = NULL, batch = NULL,
 
 #' @rdname BASiCSEstimate
 #' @export
-BASiCSEstimate.SCESet <- function(counts, spike.info = NULL, batch = NULL,
-                                  n = 20000, thin = 10, burn = 5000,
-                                  params = newBASiCSParams(), verbose = TRUE,
-                                  progress = TRUE, ...) {
+BASiCSEstimate.SingleCellExperiment <- function(counts, spike.info = NULL,
+                                                batch = NULL, n = 20000,
+                                                thin = 10, burn = 5000,
+                                                params = newBASiCSParams(),
+                                                verbose = TRUE, progress = TRUE,
+                                                ...) {
     counts <- BiocGenerics::counts(counts)
     BASiCSEstimate(counts, params)
 }

R/BASiCS-simulate.R

@@ -10,8 +10,8 @@
 #' @details
 #' This function is just a wrapper around \code{\link[BASiCS]{BASiCS_Sim}} that
 #' takes a \code{\link{BASiCSParams}}, runs the simulation then converts the
-#' output to an \code{\link[scater]{SCESet}} object. See
-#' \code{\link[BASiCS]{BASiCS_Sim}} for more details of how the simulation
+#' output to a \code{\link[SingleCellExperiment]{SingleCellExperiment}} object.
+#' See \code{\link[BASiCS]{BASiCS_Sim}} for more details of how the simulation
 #' works.
 #'
 #' @return SingleCellExperiment containing simulated counts

R/compare.R

@@ -297,7 +297,7 @@ diffSCEs <- function(sces, ref, point.size = 0.1, point.alpha = 0.1,
     for (name in names(sces)) {
         sce <- sces[[name]]
         if (!identical(dim(sce), ref.dim)) {
-            stop("SCESets must have the same dimensions")
+            stop("all datasets in 'sces' must have the same dimensions")
         }
         rowData(sce)$Dataset <- name
         colData(sce)$Dataset <- name
@@ -717,8 +717,8 @@ makeDiffPanel <- function(diff, title = "Difference comparison",
 #' \dontrun{
 #' sim1 <- splatSimulate(nGenes = 1000, batchCells = 20)
 #' sim2 <- simpleSimulate(nGenes = 1000, nCells = 20)
-#' comparison <- compSCESets(list(Splat = sim1, Simple = sim2))
-#' difference <- diffSCESets(list(Splat = sim1, Simple = sim2), ref = "Simple")
+#' comparison <- compSCEs(list(Splat = sim1, Simple = sim2))
+#' difference <- diffSCEs(list(Splat = sim1, Simple = sim2), ref = "Simple")
 #' panel <- makeOverallPanel(comparison, difference)
 #' }
 #'

index.md

@@ -16,8 +16,8 @@ data. Splatter provides a common interface to multiple simulations that have:
 * Functions for comparing simulations and real datasets
 
 Splatter is built on top of [`scater`][scater] and stores simulations in
-`SCESet` objects. Splatter also has functions for comparing simulations and real
-datasets.
+[`SingleCellExperiment`][SCE] objects. Splatter also has functions for comparing
+simulations and real datasets.
 
 **!Please note!** This site provides documentation for the development version
 of Splatter. For details on the current release please refer to
@@ -45,7 +45,7 @@ biocLite("splatter", build_vignettes=TRUE)
 ```
 
 This will also build the vignette and install all suggested dependencies (which
-aren't required for core functionality). Building the vignette may sometimes 
+aren't required for core functionality). Building the vignette may sometimes
 fail when run from the command line, if this happens try running the install
 command in RStudio.
 
@@ -73,6 +73,7 @@ devtools::install("Oshlack/splatter")
 ```
 
 [scater]: https://github.com/davismcc/scater
+[SCE]: https://github.com/drisso/SingleCellExperiment
 [bioc]: https://bioconductor.org/packages/splatter
 [devel]: https://bioconductor.org/packages/devel/bioc/html/splatter.html
 [bioc-install]: https://www.bioconductor.org/developers/how-to/useDevel/

man/BASiCSEstimate.Rd

@@ -2,7 +2,7 @@
 % Please edit documentation in R/BASiCS-estimate.R
 \name{BASiCSEstimate}
 \alias{BASiCSEstimate}
-\alias{BASiCSEstimate.SCESet}
+\alias{BASiCSEstimate.SingleCellExperiment}
 \alias{BASiCSEstimate.matrix}
 \title{Estimate BASiCS simulation parameters}
 \usage{
@@ -10,17 +10,17 @@ BASiCSEstimate(counts, spike.info = NULL, batch = NULL, n = 20000,
   thin = 10, burn = 5000, params = newBASiCSParams(), verbose = TRUE,
   progress = TRUE, ...)
 
-\method{BASiCSEstimate}{SCESet}(counts, spike.info = NULL, batch = NULL,
-  n = 20000, thin = 10, burn = 5000, params = newBASiCSParams(),
-  verbose = TRUE, progress = TRUE, ...)
+\method{BASiCSEstimate}{SingleCellExperiment}(counts, spike.info = NULL,
+  batch = NULL, n = 20000, thin = 10, burn = 5000,
+  params = newBASiCSParams(), verbose = TRUE, progress = TRUE, ...)
 
 \method{BASiCSEstimate}{matrix}(counts, spike.info = NULL, batch = NULL,
   n = 20000, thin = 10, burn = 5000, params = newBASiCSParams(),
   verbose = TRUE, progress = TRUE, ...)
 }
 \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{spike.info}{data.frame describing spike-ins with two columns: "Name"
 giving the names of the spike-in features (must match

man/BASiCSSimulate.Rd

@@ -23,8 +23,8 @@ Simulate counts using the BASiCS method.
 \details{
 This function is just a wrapper around \code{\link[BASiCS]{BASiCS_Sim}} that
 takes a \code{\link{BASiCSParams}}, runs the simulation then converts the
-output to an \code{\link[scater]{SCESet}} object. See
-\code{\link[BASiCS]{BASiCS_Sim}} for more details of how the simulation
+output to a \code{\link[SingleCellExperiment]{SingleCellExperiment}} object.
+See \code{\link[BASiCS]{BASiCS_Sim}} for more details of how the simulation
 works.
 }
 \examples{

man/makeOverallPanel.Rd

@@ -29,8 +29,8 @@ single panel.
 \dontrun{
 sim1 <- splatSimulate(nGenes = 1000, batchCells = 20)
 sim2 <- simpleSimulate(nGenes = 1000, nCells = 20)
-comparison <- compSCESets(list(Splat = sim1, Simple = sim2))
-difference <- diffSCESets(list(Splat = sim1, Simple = sim2), ref = "Simple")
+comparison <- compSCEs(list(Splat = sim1, Simple = sim2))
+difference <- diffSCEs(list(Splat = sim1, Simple = sim2), ref = "Simple")
 panel <- makeOverallPanel(comparison, difference)
 }
 

tests/testthat/test-SCESet-functions.R → tests/testthat/test-SCE-functions.R

-context("SCESet functions")
+context("SCE functions")
 
 test_that("addGeneLengths generate method works", {
     sce <- simpleSimulate()