add parallelization option to lioness (#281)

* 1.2.1 (#271) * add bioc information * update website * add crane and docs * update crane * update worflow * update crane * update workflows * update workflows * update workfolw * update workfolw * update workfolw * update workfolw * Update main.yml * Update main.yml * Update main.yml * fix lioness py * udpate lioness in R * include calculations python * update panda rm missing * update panda * update lioness joblib * revert commits * ALPACA fix to NAs in community assignement * version bump * revert lioness * update crane with alpaca changes * update lioness * update lioness python * fix test * update workflows * put back github actions * Fixed typo * Added LIONESS-pearson option + unit test * changed param labels in LIONESS example * updated docs for lioness() function * Update main.yml * Update main.yml * Update DESCRIPTION * fix crane issue #240 * expanded PANDA and LIONESS description * update crane fix * added ALPACA, EGRET, and OTTER descriptions * Update README.md * typo in na.rm * update workflow * update workflow2 * fix-actions-3 * add r lib v2 * add r lib v2 * update condor test * update condor test * update condor test * update condor test * show testthat output * add pandoc and use cache * use built in check * use built in check * update actions with built in check * bump version * use built in coverage * use built in coverage * remove sudo * update actions * update actions * removed sudo from actions * ugrade to R42 * remove virtualenv * remove virtualenv * remove virtualenv * modify condor test * update condor test * update condor test * adding retiucualte to covr * adding retiucualte to covr * add panda test to coverignore * update actions * remove lioness tests from coverage * remove lioness tests from coverage * added MONSTER and SAMBAR * remove lionessR test * Added CONDOR and YARN * Update README.md * put back otter in rbuild * remove condor test * remove condor test * remove lioness docs * add lioness to buildingore * donttest lionesss * remove coverage from ubuntu test * remove rbuilignore * update rbuildignore * update rbuildignore * update rbuildignore * update rbuildignore * update rbuildignore * add back buildignore * add back buildignore * add back buildignore * add back buildignore * add back buildignore * add back buildignore * add back buildignore * add back buildignore * add back buildignore * add back buildignore * put back tests * add padanedge diff test * add back egeret test * add monster test * fix monster test * tolerance in expect equal * tolerance in expect equal * tolerance in expect equal * tolerance in expect equal * add sourceppi * fixed PANDA tests * modify panda test * update lioness test * fix expect message * update tests * update tests * update tests * update tests * update tests * update tests * reduced lioness test data * reduced lioness test data * reduced lioness test data * reduced lioness test data * reduce test size * updating bioc (#250) * updating bioc * remove empty lines * remove empty lines * update citation * update citation * Update README.md * Update README.md * Update main.yml * Update main.yml * Update .Rbuildignore * Update .Rbuildignore * update lioness test * removed two last lioness tests * removed two last lioness tests * removed two last lioness tests * no saving of lioness networks * no saving of lioness networks * no saving of lioness networks * no saving of lioness networks * update lioness test * lower sizeof test * update test data * update test data * update test data * reduce panda tests * remove old test data * remove old test data * Update main.yml * 1.1.16 update pandapy with header argument (#260) * trying collapse readme (#261) * trying collapse readme * collapse animal description * Update README.md * update biconda (#265) * add spider (#269) * add spider * udpate spider * udpate spider * update spuder with degreeadjust * fix spider bug Co-authored-by: Kate Hoff Shutta <kshutta@umass.edu> Co-authored-by: katehoffshutta <43797774+katehoffshutta@users.noreply.github.com> * 1.2.2 (#273) - add DRAGON * add option to run lioness on multiple cores by using parallel::mclapply in place of lapply --------- Co-authored-by: Marouen <marouenbg@users.noreply.github.com> Co-authored-by: Kate Hoff Shutta <kshutta@umass.edu> Co-authored-by: katehoffshutta <43797774+katehoffshutta@users.noreply.github.com>
netZoo · Feb 22, 2023 · b397eb6 · b397eb6
1 parent 4fa7999
commit b397eb6
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Showing 2 changed files with 33 additions and 25 deletions.
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,8 +1,8 @@
 Package: netZooR
 Type: Package
 Title: Unified methods for the inference and analysis of gene regulatory networks
-Version: 1.2.1
-Date: 2022-07-07
+Version: 1.2.3
+Date: 2023-07-21
 Authors@R: c(person("Marouen", "Ben Guebila",
 			email = "benguebila@hsph.harvard.edu", role = c("aut","cre"), comment = c(ORCID = "0000-0001-5934-966X")),
 	     person("Tian", "Wang", 
@@ -37,12 +37,12 @@ biocViews:
          GraphAndNetwork
 Imports: RCy3,
 	 viridisLite, 
-   	 STRINGdb,
+   STRINGdb,
 	 Biobase,
 	 GOstats,
 	 AnnotationDbi,
-   	 matrixStats,
-   	 GO.db,
+   matrixStats,
+   GO.db,
 	 org.Hs.eg.db,
 	 Matrix,
 	 gplots,
@@ -51,21 +51,21 @@ Imports: RCy3,
 	 vegan,
 	 stats,
 	 utils,
-   	 reshape,
-   	 reshape2,
-   	 penalized,
-   	 parallel,
-   	 doParallel,
-   	 foreach,
-   	 ggplot2,
-   	 ggdendro,
-   	 grid,
-   	 MASS,
-   	 assertthat,
-   	 tidyr,
-   	 methods,
-         dplyr,
-         graphics
+   reshape,
+   reshape2,
+   penalized,
+   parallel,
+   doParallel,
+   foreach,
+   ggplot2,
+   ggdendro,
+   grid,
+   MASS,
+   assertthat,
+   tidyr,
+   methods,
+   dplyr,
+   graphics
 License: GPL-3
 Encoding: UTF-8
 LazyData: false

diff --git a/R/LIONESS.R b/R/LIONESS.R
@@ -161,13 +161,16 @@ lionessPy <- function(expr_file, motif_file=NULL, ppi_file=NULL, computing="cpu"
 #' transcription factor 2 (column 2) and a score (column 3) for the interaction.
 #' @param network.inference.method String specifying choice of network inference method. Default is "panda".
 #' Options include "pearson". 
+#' @param ncores int specifying the number of cores to be used. Default is 1. 
+#' (Note: constructing panda networks can be memory-intensive, and the number of cores should take into consideration available memory.)
 #' @param ... additional arguments for panda analysis
 #' @keywords keywords
 #' @importFrom matrixStats rowSds
 #' @importFrom matrixStats colSds
 #' @importFrom Biobase assayData
 #' @importFrom reshape melt.array
 #' @importFrom pandaR panda
+#' @importFrom parallel mclapply
 #' @export
 #' @return A list of length N, containing objects of class "panda" 
 #' corresponding to each of the N samples in the expression data set.\cr
@@ -180,25 +183,30 @@ lionessPy <- function(expr_file, motif_file=NULL, ppi_file=NULL, computing="cpu"
 #' @references
 #' Kuijjer, M.L., Tung, M., Yuan, G., Quackenbush, J. and Glass, K., 2015. 
 #' Estimating sample-specific regulatory networks. arXiv preprint arXiv:1505.06440.
-lioness = function(expr, motif = NULL, ppi = NULL, network.inference.method = "panda", ...){
+#' Kuijjer, M.L., Hsieh, PH., Quackenbush, J. et al. lionessR: single sample network inference in R. BMC Cancer 19, 1003 (2019). https://doi.org/10.1186/s12885-019-6235-7
+lioness = function(expr, motif = NULL, ppi = NULL, network.inference.method = "panda", ncores = 1, ...){
   N <- ncol(expr)
+  if(ncores < 1){
+    print('Setting number of cores to 1.')
+    ncores <- 1
+  }
   if(network.inference.method == "panda")
   {
     fullnet <- panda(motif, expr, ppi, ...)
-    return(lapply(seq_len(N), function(i) {
+    return(mclapply(seq_len(N), function(i) {
       print(paste("Computing network for sample ", i))
       N * fullnet@regNet - (N - 1) * panda(motif, expr[, -i], 
                                            ppi, ...)@regNet
-    }))
+    }, mc.cores = ncores))
   }
   if(network.inference.method == "pearson")
   {
     fullnet <- cor(t(expr))
 
-    return(lapply(seq_len(N), function(i) {
+    return(mclapply(seq_len(N), function(i) {
       print(paste("Computing network for sample ", i))
       N * fullnet - (N - 1) * cor(t(expr[,-i]))
-    }))
+    }, mc.cores = ncores))
   }
   if(!(network.inference.method %in% c("panda","pearson")))
   {