rewritten parallelism to BiocParallel package

DESCRIPTION

@@ -1,34 +1,66 @@
-Package: SC3
 Type: Package
+Package: SC3
 Title: Single-Cell Consensus Clustering
 Version: 1.15.1
+Authors@R: 
+    c(person(given = "Vladimir",
+             family = "Kiselev",
+             role = c("cre", "aut"),
+             email = "[email protected]"),
+      person(given = "Andrew",
+             family = "Yiu",
+             role = "ctb"),
+      person(given = "Tallulah",
+             family = "Andrews",
+             role = "ctb"),
+      person(given = "Martin",
+             family = "Hemberg",
+             role = "aut"))
 Author: Vladimir Kiselev
 Maintainer: Vladimir Kiselev <[email protected]>
-Authors@R: c(person("Vladimir", "Kiselev",
-             email = "[email protected]",
-             role=c("cre", "aut")),
-             person("Andrew", "Yiu",
-             role=c("ctb")),
-             person("Tallulah", "Andrews",
-             role=c("ctb")),
-             person("Martin", "Hemberg",
-             role=c("aut")))
-Description: A tool for unsupervised clustering and analysis of single cell RNA-Seq data.
+Description: A tool for unsupervised clustering and analysis of single
+    cell RNA-Seq data.
 License: GPL-3
-Imports: graphics, stats, utils, methods, e1071, parallel, foreach,
-          doParallel, doRNG, shiny, ggplot2, pheatmap (>= 1.0.8),
-          ROCR, robustbase, rrcov, cluster, WriteXLS,
-          Rcpp (>= 0.11.1), SummarizedExperiment, SingleCellExperiment,
-          BiocGenerics, S4Vectors
-Depends: R(>= 3.3)
-LinkingTo: Rcpp, RcppArmadillo
-LazyData: TRUE
-RoxygenNote: 6.0.1
-Suggests: knitr, rmarkdown, mclust, scater
-VignetteBuilder: knitr
-biocViews: ImmunoOncology, SingleCell, Software, Classification, Clustering, DimensionReduction, 
-            SupportVectorMachine, RNASeq, Visualization, Transcriptomics, 
-            DataRepresentation, GUI, DifferentialExpression, Transcription
-NeedsCompilation: no
 URL: https://github.com/hemberg-lab/SC3
 BugReports: https://support.bioconductor.org/t/sc3/
+Depends: 
+    R (>= 3.3)
+Imports: 
+    BiocGenerics,
+    BiocParallel,
+    cluster,
+    e1071,
+    ggplot2,
+    graphics,
+    methods,
+    pheatmap (>= 1.0.8),
+    Rcpp (>= 0.11.1),
+    robustbase,
+    ROCR,
+    rrcov,
+    S4Vectors,
+    shiny,
+    SingleCellExperiment,
+    stats,
+    SummarizedExperiment,
+    utils,
+    WriteXLS
+Suggests: 
+    BiocStyle,
+    knitr,
+    mclust,
+    rmarkdown,
+    scater
+LinkingTo: 
+    Rcpp,
+    RcppArmadillo
+VignetteBuilder: 
+    knitr
+biocViews: ImmunoOncology, SingleCell, Software, Classification,
+    Clustering, DimensionReduction, SupportVectorMachine, RNASeq,
+    Visualization, Transcriptomics, DataRepresentation, GUI,
+    DifferentialExpression, Transcription
+Encoding: UTF-8
+LazyData: TRUE
+NeedsCompilation: no
+RoxygenNote: 7.1.1

NAMESPACE

@@ -39,11 +39,7 @@ importFrom(SummarizedExperiment,assayNames)
 importFrom(SummarizedExperiment,colData)
 importFrom(SummarizedExperiment,rowData)
 importFrom(WriteXLS,WriteXLS)
-importFrom(doParallel,registerDoParallel)
-importFrom(doRNG,"%dorng%")
 importFrom(e1071,svm)
-importFrom(foreach,"%dopar%")
-importFrom(foreach,foreach)
 importFrom(ggplot2,aes)
 importFrom(ggplot2,geom_bar)
 importFrom(ggplot2,ggplot)
@@ -53,9 +49,6 @@ importFrom(ggplot2,ylim)
 importFrom(graphics,plot)
 importFrom(methods,as)
 importFrom(methods,new)
-importFrom(parallel,detectCores)
-importFrom(parallel,makeCluster)
-importFrom(parallel,stopCluster)
 importFrom(pheatmap,pheatmap)
 importFrom(robustbase,covMcd)
 importFrom(rrcov,PcaHubert)

R/AllGenerics.R

@@ -1,49 +1,48 @@
 #' @export
-setGeneric("sc3", signature = "object", function(object, ks = NULL, 
-        gene_filter = TRUE, pct_dropout_min = 10, pct_dropout_max = 90, 
-        d_region_min = 0.04, d_region_max = 0.07, svm_num_cells = NULL, 
-        svm_train_inds = NULL, svm_max = 5000, n_cores = NULL, kmeans_nstart = NULL, 
-        kmeans_iter_max = 1e+09, k_estimator = FALSE, biology = FALSE, rand_seed = 1) {
+setGeneric("sc3", signature = "object", function(object, ks = NULL,
+        gene_filter = TRUE, pct_dropout_min = 10, pct_dropout_max = 90,
+        d_region_min = 0.04, d_region_max = 0.07, svm_num_cells = NULL,
+        svm_train_inds = NULL, svm_max = 5000, kmeans_nstart = NULL,
+        kmeans_iter_max = 1e+09, k_estimator = FALSE, biology = FALSE,
+        BPPARAM = BiocParallel::bpparam()) {
     standardGeneric("sc3")
 })
 
 #' @export
-setGeneric("sc3_estimate_k", signature = "object", function(object) {
+setGeneric("sc3_estimate_k", signature = "object", function(object, BPPARAM = BiocParallel::bpparam()) {
     standardGeneric("sc3_estimate_k")
 })
 
 #' @export
-setGeneric("sc3_prepare", function(object, gene_filter = TRUE, 
-        pct_dropout_min = 10, pct_dropout_max = 90, d_region_min = 0.04, 
-        d_region_max = 0.07, svm_num_cells = NULL, svm_train_inds = NULL, 
-        svm_max = 5000, n_cores = NULL, kmeans_nstart = NULL, 
-        kmeans_iter_max = 1e+09, rand_seed = 1) {
+setGeneric("sc3_prepare", function(object, gene_filter = TRUE,
+        pct_dropout_min = 10, pct_dropout_max = 90, d_region_min = 0.04,
+        d_region_max = 0.07, svm_num_cells = NULL, svm_train_inds = NULL,
+        svm_max = 5000, kmeans_nstart = NULL, kmeans_iter_max = 1e+09) {
     standardGeneric("sc3_prepare")
 })
 
 #' @export
-setGeneric("sc3_calc_dists", signature = "object", function(object) {
+setGeneric("sc3_calc_dists", signature = "object", function(object, BPPARAM = BiocParallel::bpparam()) {
     standardGeneric("sc3_calc_dists")
 })
 
 #' @export
-setGeneric("sc3_calc_transfs", signature = "object", function(object) {
+setGeneric("sc3_calc_transfs", signature = "object", function(object, BPPARAM = BiocParallel::bpparam()) {
     standardGeneric("sc3_calc_transfs")
 })
 
 #' @export
-setGeneric("sc3_kmeans", signature = "object", function(object, ks = NULL) {
+setGeneric("sc3_kmeans", signature = "object", function(object, ks = NULL, BPPARAM = BiocParallel::bpparam()) {
     standardGeneric("sc3_kmeans")
 })
 
 #' @export
-setGeneric("sc3_calc_consens", signature = "object", function(object) {
+setGeneric("sc3_calc_consens", signature = "object", function(object, BPPARAM = BiocParallel::bpparam()) {
     standardGeneric("sc3_calc_consens")
 })
 
 #' @export
-setGeneric("sc3_calc_biology", signature = "object", function(object, ks = NULL, 
-                                                              regime = NULL) {
+setGeneric("sc3_calc_biology", signature = "object", function(object, ks = NULL, regime = NULL, BPPARAM = BiocParallel::bpparam()) {
     standardGeneric("sc3_calc_biology")
 })
 
@@ -58,7 +57,7 @@ setGeneric("sc3_run_svm", signature = "object", function(object, ks = NULL) {
 })
 
 #' @export
-setGeneric("sc3_plot_consensus", signature = "object", function(object, k, 
+setGeneric("sc3_plot_consensus", signature = "object", function(object, k,
                                                                 show_pdata = NULL) {
     standardGeneric("sc3_plot_consensus")
 })
@@ -74,13 +73,13 @@ setGeneric("sc3_plot_expression", signature = "object", function(object, k, show
 })
 
 #' @export
-setGeneric("sc3_plot_de_genes", signature = "object", function(object, 
+setGeneric("sc3_plot_de_genes", signature = "object", function(object,
                                         k, p.val = 0.01, show_pdata = NULL) {
     standardGeneric("sc3_plot_de_genes")
 })
 
 #' @export
-setGeneric("sc3_plot_markers", signature = "object", function(object, k, auroc = 0.85, 
+setGeneric("sc3_plot_markers", signature = "object", function(object, k, auroc = 0.85,
                                         p.val = 0.01, show_pdata = NULL) {
     standardGeneric("sc3_plot_markers")
 })
@@ -91,7 +90,7 @@ setGeneric("sc3_plot_cluster_stability", signature = "object", function(object,
 })
 
 #' @export
-setGeneric("sc3_export_results_xls", signature = "object", function(object, 
+setGeneric("sc3_export_results_xls", signature = "object", function(object,
                                                 filename = "sc3_results.xls") {
     standardGeneric("sc3_export_results_xls")
 })