Updated summarizeQueryRegionsMulti function with additional import st…

…atements and documentation

NAMESPACE

@@ -54,6 +54,8 @@ importFrom(genomation,ScoreMatrix)
 importFrom(genomation,ScoreMatrixBin)
 importFrom(org.Hs.eg.db,org.Hs.egENSEMBL2EG)
 importFrom(parallel,clusterCall)
+importFrom(parallel,clusterEvalQ)
+importFrom(parallel,clusterExport)
 importFrom(parallel,makeCluster)
 importFrom(parallel,stopCluster)
 importFrom(pbapply,pbsapply)

R/meta_analysis_functions.R

@@ -57,13 +57,26 @@ importBedFiles <- function(filePaths, ...) {
 #' summaryMatrix <- summarizeQueryRegionsMulti(queryRegionsList = queryRegionsList,
 #'                                  txdbFeatures = txdbFeatures)
 #'
+#' @importFrom parallel makeCluster
+#' @importFrom parallel clusterExport
+#' @importFrom parallel clusterEvalQ
+#' @importFrom pbapply pbsapply 
 #' @export
-summarizeQueryRegionsMulti <- function(queryRegionsList, txdbFeatures) {
-  summaryRaw <- sapply(queryRegionsList, function(x) summarizeQueryRegions(x, txdbFeatures))
-  rownames(summaryRaw) <- names(txdbFeatures)
+summarizeQueryRegionsMulti <- function(queryRegionsList, txdbFeatures, nodeN = 1) {
+  cl <- parallel::makeCluster(nodeN)
+  parallel::clusterExport(cl = cl, 
+                          varlist = c('txdbFeatures', 'summarizeQueryRegions'), 
+                          envir = environment())
+  summaryRaw <- pbapply::pbsapply(queryRegionsList, 
+                                  function(x) {
+                                    summarizeQueryRegions(x, txdbFeatures)
+                                    }, cl = cl)
+  rownames(summaryRaw) <- c(names(txdbFeatures), 'NoFeatures')
+  stopCluster(cl)
   return(t(summaryRaw))
 }
 
+
 #' getOverlapSimilarityMatrix
 #' 
 #' This function takes as input a GRangesList object and finds pairwise

RCAS.Rproj

@@ -15,3 +15,4 @@ LaTeX: pdfLaTeX
 BuildType: Package
 PackageUseDevtools: Yes
 PackageInstallArgs: --no-multiarch --with-keep.source
+PackageRoxygenize: rd,collate,namespace,vignette