Add BPPARAM to scDDSimulate

R/scDD-simulate.R

@@ -7,6 +7,9 @@
 #' plots.
 #' @param plot.file File path to save plots as PDF.
 #' @param verbose logical. Whether to print 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 ... any additional parameter settings to override what is provided in
 #'        \code{params}.
 #'
@@ -33,8 +36,10 @@
 #' }
 #' @export
 #' @importFrom scater newSCESet
+#' @importFrom BiocParallel SerialParam
 scDDSimulate <- function(params = newSCDDParams(), plots = FALSE,
-                         plot.file = NULL, verbose = TRUE, ...) {
+                         plot.file = NULL, verbose = TRUE,
+                         BPPARAM = SerialParam(), ...) {
 
     checkmate::assertClass(params, "SCDDParams")
     params <- setParams(params, ...)
@@ -62,7 +67,8 @@ scDDSimulate <- function(params = newSCDDParams(), plots = FALSE,
                                       plot.file = plot.file,
                                       random.seed = getParam(params, "seed"),
                                       varInflation = varInflation,
-                                      condition = getParam(params, "condition"))
+                                      condition = getParam(params, "condition"),
+                                      param = BPPARAM)
     } else {
         suppressMessages(
         scDD.sim <- scDD::simulateSet(SCdat = getParam(params, "SCdat"),
@@ -79,7 +85,8 @@ scDDSimulate <- function(params = newSCDDParams(), plots = FALSE,
                                       plot.file = plot.file,
                                       random.seed = getParam(params, "seed"),
                                       varInflation = varInflation,
-                                      condition = getParam(params, "condition"))
+                                      condition = getParam(params, "condition"),
+                                      param = BPPARAM)
         )
     }
 

man/scDDSimulate.Rd

@@ -5,7 +5,7 @@
 \title{scDD simulation}
 \usage{
 scDDSimulate(params = newSCDDParams(), plots = FALSE, plot.file = NULL,
-  verbose = TRUE, ...)
+  verbose = TRUE, BPPARAM = SerialParam(), ...)
 }
 \arguments{
 \item{params}{SCDDParams object containing simulation parameters.}
@@ -17,6 +17,10 @@ plots.}
 
 \item{verbose}{logical. Whether to print progress messages}
 
+\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{...}{any additional parameter settings to override what is provided in
 \code{params}.}
 }