diff --git a/NAMESPACE b/NAMESPACE
index 216436b18d78a343574efa2442f5243c0a6454b0..16a874dc59cc293733ab91688904545878cf5ff6 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -5,6 +5,7 @@ S3method(lun2Estimate,matrix)
S3method(lunEstimate,SingleCellExperiment)
S3method(lunEstimate,matrix)
S3method(scDDEstimate,SingleCellExperiment)
+S3method(scDDEstimate,default)
S3method(scDDEstimate,matrix)
S3method(simpleEstimate,SingleCellExperiment)
S3method(simpleEstimate,matrix)
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/R/scDD-estimate.R b/R/scDD-estimate.R
index 7253c61e01dda32fbac1cba7c14324fafb05142f..9c213670a4aec8d72f1c08305aa4c4894e1f3fbb 100644
--- a/R/scDD-estimate.R
+++ b/R/scDD-estimate.R
@@ -6,11 +6,14 @@
#' 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 condition String giving the column that represents biological group of
+#' interest.
#' @param params SCDDParams object to store estimated values in.
#' @param verbose logical. Whether to show progress messages.
#' @param BPPARAM A \code{\link[BiocParallel]{BiocParallelParam}} instance
#' giving the parallel back-end to be used. Default is
#' \code{\link[BiocParallel]{SerialParam}} which uses a single core.
+#' @param ... further arguments passed to or from other methods.
#'
#' @details
#' This function applies \code{\link[scDD]{preprocess}} to the counts then uses
@@ -29,64 +32,75 @@
#' }
#' @importFrom BiocParallel SerialParam
#' @export
-scDDEstimate <- function(counts, conditions, params = newSCDDParams(),
- verbose = TRUE, BPPARAM = SerialParam()) {
+scDDEstimate <- function(counts, #conditions, condition,
+ params = newSCDDParams(), verbose = TRUE,
+ BPPARAM = SerialParam(), ...) {
+
+ if (!requireNamespace("scDD", quietly = TRUE)) {
+ stop("The scDD simulation requires the 'scDD' package.")
+ }
+
UseMethod("scDDEstimate")
}
+#' @rdname scDDEstimate
+#' @importFrom SingleCellExperiment SingleCellExperiment
+#' @export
+scDDEstimate.matrix <- function(counts, params = newSCDDParams(),
+ verbose = TRUE, BPPARAM = SerialParam(),
+ conditions, ...) {
+
+ checkmate::assertMatrix(counts, mode = "numeric", any.missing = FALSE,
+ min.rows = 1, min.cols = 1, row.names = "unique",
+ col.names = "unique")
+ checkmate::assertIntegerish(conditions, len = ncol(counts), lower = 1,
+ upper = 2)
+
+ counts <- SingleCellExperiment(assays = list(counts = counts),
+ colData = data.frame(condition = conditions))
+ scDDEstimate.default(counts, "condition", params, verbose, BPPARAM)
+}
+
#' @rdname scDDEstimate
#' @export
-scDDEstimate.SingleCellExperiment <- function(counts, conditions,
+scDDEstimate.SingleCellExperiment <- function(counts,
params = newSCDDParams(),
verbose = TRUE,
- BPPARAM = SerialParam()) {
- counts <- BiocGenerics::counts(counts)
- scDDEstimate(counts, conditions, params, verbose, BPPARAM)
+ BPPARAM = SerialParam(),
+ condition = "condition", ...) {
+ scDDEstimate.default(counts, condition, params, verbose, BPPARAM)
}
#' @rdname scDDEstimate
#' @importFrom methods as
#' @export
-scDDEstimate.matrix <- function(counts, conditions, params = newSCDDParams(),
- verbose = TRUE, BPPARAM = SerialParam()) {
-
- if (!requireNamespace("scDD", quietly = TRUE)) {
- stop("The scDD simulation requires the 'scDD' package.")
- }
+scDDEstimate.default <- function(counts,
+ params = newSCDDParams(), verbose = TRUE,
+ BPPARAM = SerialParam(), condition, ...) {
checkmate::assertClass(params, "SCDDParams")
- checkmate::assertMatrix(counts, mode = "numeric", any.missing = FALSE,
- min.rows = 1, min.cols = 1, row.names = "unique",
- col.names = "unique")
- checkmate::assertIntegerish(conditions, len = ncol(counts), lower = 1,
- upper = 2)
-
- counts.list <- list(Cond1 = counts[, conditions == 1],
- Cond2 = counts[, conditions == 2])
+ checkmate::assertClass(counts, "SingleCellExperiment")
+ checkmate::assertCharacter(condition, min.chars = 1, any.missing = FALSE,
+ len = 1)
+ if (!(condition %in% colnames(SummarizedExperiment::colData(counts)))) {
+ stop("'condition' must be the name of a column in `colData(counts)`")
+ }
if (verbose) {
- processed <- scDD::preprocess(counts.list, c("Cond1", "Cond2"),
- median_norm = TRUE)
+ processed <- scDD::preprocess(counts, condition, median_norm = TRUE)
} else {
suppressMessages(
- processed <- scDD::preprocess(counts.list, c("Cond1", "Cond2"),
- median_norm = TRUE)
+ processed <- scDD::preprocess(counts, condition, median_norm = TRUE)
)
}
- assays <- S4Vectors::SimpleList(NormCounts = processed)
-
- colData <- S4Vectors::DataFrame(condition = conditions,
- row.names = colnames(processed))
-
- SCdat <- SummarizedExperiment::SummarizedExperiment(assays = assays,
- colData = colData)
-
if (verbose) {
- SCdat <- scDD::scDD(SCdat, testZeroes = FALSE, param = BPPARAM)
+ SCdat <- scDD::scDD(processed, testZeroes = FALSE, param = BPPARAM,
+ condition = condition)
} else {
dummy <- utils::capture.output(suppressMessages(
- SCdat <- scDD::scDD(SCdat, testZeroes = FALSE, param = BPPARAM)
+ SCdat <- scDD::scDD(processed, testZeroes = FALSE, param = BPPARAM,
+ condition = condition)
))
}
diff --git a/R/scDD-simulate.R b/R/scDD-simulate.R
index 704e14af1eb4d129e8b7411e025c5d21a5292de2..a9dbd3fec07b80631c68f08886fba38fc9c8fdb9 100644
--- a/R/scDD-simulate.R
+++ b/R/scDD-simulate.R
@@ -91,9 +91,9 @@ scDDSimulate <- function(params = newSCDDParams(), plots = FALSE,
)
}
- counts <- scDD.sim[[1]]
- foldchanges <- scDD.sim[[2]]
- de.status <- rownames(counts)
+ counts <- SummarizedExperiment::assays(scDD.sim)$normcounts
+ foldchanges <- SummarizedExperiment::rowData(scDD.sim)$FC
+ de.status <- SummarizedExperiment::rowData(scDD.sim)$Category
if (verbose) {message("Creating final dataset...")}
cell.names <- paste0("Cell", seq_len(nCells * 2))
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}}.
}
diff --git a/man/scDDEstimate.Rd b/man/scDDEstimate.Rd
index 6eb052e2e0bcbf8a587701f2fdccf7f1bf38373e..265183465ffcd3ca73550931c721146c38f57611 100644
--- a/man/scDDEstimate.Rd
+++ b/man/scDDEstimate.Rd
@@ -2,26 +2,27 @@
% Please edit documentation in R/scDD-estimate.R
\name{scDDEstimate}
\alias{scDDEstimate}
-\alias{scDDEstimate.SingleCellExperiment}
\alias{scDDEstimate.matrix}
+\alias{scDDEstimate.SingleCellExperiment}
+\alias{scDDEstimate.default}
\title{Estimate scDD simulation parameters}
\usage{
-scDDEstimate(counts, conditions, params = newSCDDParams(), verbose = TRUE,
- BPPARAM = SerialParam())
+scDDEstimate(counts, params = newSCDDParams(), verbose = TRUE,
+ BPPARAM = SerialParam(), ...)
+
+\method{scDDEstimate}{matrix}(counts, params = newSCDDParams(),
+ verbose = TRUE, BPPARAM = SerialParam(), conditions, ...)
-\method{scDDEstimate}{SingleCellExperiment}(counts, conditions,
- params = newSCDDParams(), verbose = TRUE, BPPARAM = SerialParam())
+\method{scDDEstimate}{SingleCellExperiment}(counts, params = newSCDDParams(),
+ verbose = TRUE, BPPARAM = SerialParam(), condition = "condition", ...)
-\method{scDDEstimate}{matrix}(counts, conditions, params = newSCDDParams(),
- verbose = TRUE, BPPARAM = SerialParam())
+\method{scDDEstimate}{default}(counts, params = newSCDDParams(),
+ verbose = TRUE, BPPARAM = SerialParam(), condition, ...)
}
\arguments{
\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.}
-
\item{params}{SCDDParams object to store estimated values in.}
\item{verbose}{logical. Whether to show progress messages.}
@@ -29,6 +30,14 @@ Conditions can be 1 or 2.}
\item{BPPARAM}{A \code{\link[BiocParallel]{BiocParallelParam}} instance
giving the parallel back-end to be used. Default is
\code{\link[BiocParallel]{SerialParam}} which uses a single core.}
+
+\item{...}{further arguments passed to or from other methods.}
+
+\item{conditions}{Vector giving the condition that each cell belongs to.
+Conditions can be 1 or 2.}
+
+\item{condition}{String giving the column that represents biological group of
+interest.}
}
\value{
SCDDParams object containing the estimated parameters.