Update scDDEstimate

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)

R/scDD-estimate.R

@@ -6,6 +6,8 @@
 #'        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
@@ -29,64 +31,70 @@
 #' }
 #' @importFrom BiocParallel SerialParam
 #' @export
-scDDEstimate <- function(counts, conditions, params = newSCDDParams(),
-                         verbose = TRUE, BPPARAM = SerialParam()) {
+scDDEstimate <- function(counts, 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, conditions, params = newSCDDParams(),
+                                verbose = TRUE, BPPARAM = SerialParam(), ...) {
+
+    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, condition = "condition",
                                               params = newSCDDParams(),
                                               verbose = TRUE,
-                                              BPPARAM = SerialParam()) {
-    counts <- BiocGenerics::counts(counts)
-    scDDEstimate(counts, conditions, params, verbose, BPPARAM)
+                                              BPPARAM = SerialParam(), ...) {
+    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, condition, params, verbose, BPPARAM) {
 
     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)
         ))
     }
 

man/scDDEstimate.Rd

@@ -2,26 +2,26 @@
 % 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())
-
-\method{scDDEstimate}{SingleCellExperiment}(counts, conditions,
-  params = newSCDDParams(), verbose = TRUE, BPPARAM = SerialParam())
+scDDEstimate(counts, params = newSCDDParams(), verbose = TRUE,
+  BPPARAM = SerialParam(), ...)
 
 \method{scDDEstimate}{matrix}(counts, conditions, params = newSCDDParams(),
-  verbose = TRUE, BPPARAM = SerialParam())
+  verbose = TRUE, BPPARAM = SerialParam(), ...)
+
+\method{scDDEstimate}{SingleCellExperiment}(counts, condition = "condition",
+  params = newSCDDParams(), verbose = TRUE, BPPARAM = SerialParam(), ...)
+
+\method{scDDEstimate}{default}(counts, condition, params, verbose, BPPARAM)
 }
 \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 +29,12 @@ 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{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.