v1.1.1

Updated version numbering to match Bioc conventions

JunctionSeq/DESCRIPTION

@@ -1,5 +1,5 @@
 Package: JunctionSeq
-Version: 1.0.0
+Version: 1.1.1
 Title: JunctionSeq: A Utility for Detection of Differential Exon and Splice-Junction Usage in RNA-Seq data
 Authors@R: c(person("Stephen", "Hartley", role = c("aut", "cre"),
            email = "[email protected]", comment = "PhD"),

JunctionSeq/R/00.minor.utils.R

@@ -442,16 +442,17 @@ getMyApply <- function(nCores = 1, verbose = TRUE, allowWindowsMulticore = TRUE,
      #BiocParallel.package.found <- TRUE; #suppressMessages(suppressWarnings(require("BiocParallel")))
 
      if( Sys.info()[['sysname']] == 'Windows' ){
-       message(">>> NOTE: Microsoft windows detected. As of BiocParallel v1.2.0 and R 3.1.1, simple multicore forking is not supported on windows. ")
-       message("          JunctionSeq will fall-back to single-core operation if necessary.")
+       if(verbose) message(">>> NOTE: Microsoft windows detected. As of BiocParallel v1.2.0 and R 3.1.1, simple multicore forking is not supported on windows. ")
+       if(verbose) message("          JunctionSeq will fall-back to single-core operation if necessary.")
      } 
 
-       message("    [[Using package \"BiocParallel\" for parallelization. (Using ",nCores," cores)]]")
+       if(verbose) message("    [[Using package \"BiocParallel\" for parallelization. (Using ",nCores," cores)]]")
        if( Sys.info()[['sysname']] == 'Windows' ){
-         message(">>> WARNING: attempting to use BiocParallel for multicore functionality. However: On windows machines some versions of BiocParallel appear to run very slowly and do not appear to actually use multiple cores.")
+         if(verbose) message(">>> WARNING: attempting to use BiocParallel for multicore functionality. However: On windows machines some versions of BiocParallel appear to run very slowly and do not appear to actually use multiple cores.")
        }
        myApply <- function(X, FUN){ BiocParallel::bplapply( X, FUN, BPPARAM = BiocParallel::MulticoreParam(workers = nCores) ) }
    } else {
+     if(verbose) message("> Using single-core execution.")
      myApply <- lapply
    }
 
@@ -472,6 +473,18 @@ getMyApply <- function(nCores = 1, verbose = TRUE, allowWindowsMulticore = TRUE,
    return(myApply)
 }
 
+getBPParam <- function(nCores = 1){
+   if(! is.numeric(nCores)){
+     if(is(nCores, "BiocParallelParam")){
+       return(nCores);
+     } else {
+       stop("Fatal Error: nCores must be either an integer or a BiocParallelParam object")
+     }
+   } else {
+     return(MulticoreParam(workers=nCores));
+   }
+}
+
 ##########################################################################
 ######### Front-end Utility Functions:
 ##########################################################################

JunctionSeq/R/main.analysis.R

@@ -564,7 +564,9 @@ estimateJunctionSeqDispersions <- function( jscs,
      mcols(jscs@DESeqDataSet)$baseVar <- fData(jscs)$baseVar
    } else {
      dds <- jscs@DESeqDataSet
-     dds <- estimateUnsharedDispersions( dds, formula=test.formula1, BPPARAM=MulticoreParam(workers=nCores), quiet= !verbose)
+     if(verbose) message("---------> Executing DESeq2 call: estimateUnsharedDispersions");
+     dds <- estimateUnsharedDispersions( dds, formula=test.formula1, BPPARAM=getBPParam(nCores), quiet= !verbose)
+     if(verbose) message("---------> Finished with DESeq2 call.");
      fData(jscs)$dispBeforeSharing <- mcols(dds)$dispGeneEst
      mcols(dds)$baseMean <- fData(jscs)$baseMean
      mcols(dds)$baseVar <- fData(jscs)$baseVar
@@ -634,7 +636,7 @@ testForDiffUsage <- function( jscs,
        warning("Saving Hypothesis Test Model Fits is Deprecated with DESeq2-style hypothesis testing.")
      }
 
-     BPPARAM <- MulticoreParam(workers = nCores)
+     BPPARAM <- getBPParam(nCores);
      reducedModelMatrix <- mm0
      fullModelMatrix <- mm1
      object <- jscs@DESeqDataSet

JunctionSeq/vignettes/JunctionSeq.Rnw

@@ -389,7 +389,7 @@ jscs <- runJunctionSeqAnalyses(sample.files = countFiles,
                            sample.names = decoder$sample.ID, 
                            condition=factor(decoder$group.ID),
                            flat.gff.file = gff.file,
-                           nCores = 6,
+                           nCores = 1,
                            analysis.type = "junctionsAndExons"
                            );
 @
@@ -453,7 +453,7 @@ jscs <- estimateJunctionSeqSizeFactors(jscs);
 
 Next, we generate test-specific dispersion estimates:
 <<testStep3, results="hide", warning=FALSE>>=
-jscs <- estimateJunctionSeqDispersions(jscs, nCores = 6);
+jscs <- estimateJunctionSeqDispersions(jscs, nCores = 1);
 @
 
 Next, we fit these observed dispersions to a regression to create fitted dispersions:
@@ -463,12 +463,12 @@ jscs <- fitJunctionSeqDispersionFunction(jscs);
 
 Next, we perform the hypothesis tests for differential splice junction usage:
 <<testStep5, results="hide", warning=FALSE>>=
-jscs <- testForDiffUsage(jscs, nCores = 6); 
+jscs <- testForDiffUsage(jscs, nCores = 1); 
 @
 
 Finally, we calculate effect sizes and parameter estimates:
 <<testStep6, results="hide", warning=FALSE>>=
-jscs <- estimateEffectSizes( jscs, nCores = 6); 
+jscs <- estimateEffectSizes( jscs, nCores = 1); 
 @
 
 All these steps simply duplicates the behavior of the runJunctionSeqAnalyses function. However, far more options are available when run in this way. Full documentation of the various options for these commands:
@@ -1040,7 +1040,7 @@ jscs.DEX <- runJunctionSeqAnalyses(sample.files = countFiles,
                   sample.names = decoder$sample.ID,
                   condition = factor(decoder$group.ID),
                   flat.gff.file = gff.file, 
-                  nCores = 6,
+                  nCores = 1,
                   analysis.type = "exonsOnly",
                   method.countVectors = "sumOfAllBinsForGene",
                   method.sizeFactors = "byCountbins",
@@ -1118,7 +1118,7 @@ jscs <- runJunctionSeqAnalyses(sample.files = countFiles,
                            sample.names = decoder$sample.ID, 
                            condition=factor(threeLevelVariable),
                            flat.gff.file = gff.file,
-                           nCores = 6,
+                           nCores = 1,
                            analysis.type = "junctionsAndExons"
                            );
 @
@@ -1146,7 +1146,7 @@ jscs <- runJunctionSeqAnalyses(sample.files = countFiles.8,
                            condition= decoder.8$condition,
                            use.covars = decoder.8[,"smokeStatus",drop=F],
                            flat.gff.file = gff.file,
-                           nCores = 6,
+                           nCores = 1,
                            analysis.type = "junctionsAndExons",
 test.formula0  = ~ sample + countbin + smokeStatus : countbin, 
 test.formula1  = ~ sample + countbin + smokeStatus : countbin + condition : countbin,

README.md

@@ -1,5 +1,5 @@
 # JunctionSeq
-    > v1.0.0 (Revised Sun Jan 31 13:36:15 EST 2016)
+    > v1.1.1 (Revised Mon Feb  1 10:18:54 EST 2016)
 
 [Help, documentation, and the most recent release of JunctionSeq is available on the JunctionSeq github page](http://hartleys.github.io/JunctionSeq/).
 

buildLogs/EXDATA-R-CMD-build-LINUX-R-v3.2.2.log

@@ -1,4 +1,4 @@
------ R CMD build (Sun Jan 31 13:42:59 EST 2016)          -----
+----- R CMD build (Mon Feb  1 10:19:16 EST 2016)          -----
 R version 3.2.2 (2015-08-14) -- "Fire Safety"
 Copyright (C) 2015 The R Foundation for Statistical Computing
 Platform: x86_64-pc-linux-gnu (64-bit)
@@ -9,7 +9,7 @@ GNU General Public License versions 2 or 3.
 For more information about these matters see
 http://www.gnu.org/licenses/.
 
------ R CMD build STARTING (Sun Jan 31 13:42:59 EST 2016) -----
+----- R CMD build STARTING (Mon Feb  1 10:19:16 EST 2016) -----
 * checking for file '/cluster/ifs/users/mullikin/Klein/steve/projects/ZZZ-ExampleDataset/TestSets/QoRTsPipelineWalkthrough/outputData/JctSeqData/DESCRIPTION' ... OK
 * preparing 'JctSeqData':
 * checking DESCRIPTION meta-information ... OK
@@ -19,6 +19,6 @@ http://www.gnu.org/licenses/.
 * checking for empty or unneeded directories
 * looking to see if a 'data/datalist' file should be added
 * re-saving image files
-* building 'JctSeqData_1.0.0.tar.gz'
+* building 'JctSeqData_1.1.1.tar.gz'
 
------ R CMD build COMPLETE (Sun Jan 31 13:44:41 EST 2016) -----
+----- R CMD build COMPLETE (Mon Feb  1 10:20:51 EST 2016) -----