Use S3 and S4 methods (#28)

* use S3 and S4 methods for shared functionality across packages (e.g. FRASER)
* version bump: 1.7.0 -> 1.7.1

* CI fixes
  ** adapt to the new knitr update braking BiocStyle in R3.6
  ** no cache on appveyor
  ** just test r-release on windows (appveyor)

.travis.yml

@@ -39,17 +39,16 @@ before_install:
   - tlmgr install index marginfix bera nowidow parnotes
 
 install:
-  - R --version
   - Rscript setupEnv.R
-
+  - R --version
+  - R -e "BiocManager::version()"
 
 script:
   - R CMD build .
   - R -e 'BiocCheck::BiocCheck(".", `no-check-vignettes`=TRUE)'
   - R CMD check --no-vignettes --timings *tar.gz
-  - R -e 'devtools::run_examples()'
+  - R -e 'devtools::run_examples(run=TRUE, document=TRUE)'
   - cd vignettes && R CMD Sweave --engine=knitr::knitr --pdf OUTRIDER.Rnw
 
-
 after_success:
   - test $TRAVIS_BUILD_STAGE_NAME = "Test" && Rscript -e 'covr::codecov()'

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: OUTRIDER
 Title: OUTRIDER - OUTlier in RNA-Seq fInDER
 Type: Package
-Version: 1.7.0
+Version: 1.7.1
 Date: 2020-04-13
 URL: https://github.com/gagneurlab/OUTRIDER
 BugRepots: https://github.com/gagneurlab/OUTRIDER/issues
@@ -27,7 +27,7 @@ biocViews: ImmunoOncology, RNASeq, Transcriptomics, Alignment, Sequencing,
 License: MIT + file LICENSE
 NeedsCompilation: yes
 Encoding: UTF-8
-RoxygenNote: 7.1.0
+RoxygenNote: 7.1.1
 Depends:
     R (>= 3.6), 
     BiocParallel,
@@ -37,16 +37,14 @@ Depends:
     methods
 Imports:
     BBmisc,
-    Biobase,
     BiocGenerics,
-    compiler,
     DESeq2 (>= 1.16.1),
+    generics,
     GenomicRanges,
     ggplot2,
     grDevices,
     heatmaply,
     pheatmap,
-    gplots,
     graphics,
     IRanges,
     matrixStats,
@@ -79,6 +77,7 @@ LinkingTo:
 Collate:
     package-OUTRIDER.R
     class-OutriderDataSet.R
+    AllGenerics.R
     inputCheckerFunctions.R
     helperFunctions.R
     getNSetterFuns.R

NAMESPACE

@@ -1,5 +1,6 @@
 # Generated by roxygen2: do not edit by hand
 
+S3method(fit,OutriderDataSet)
 export("counts<-")
 export("normalizationFactors<-")
 export("sampleExclusionMask<-")
@@ -17,6 +18,7 @@ export(estimateSizeFactors)
 export(filterExpression)
 export(findEncodingDim)
 export(findInjectZscore)
+export(fit)
 export(fpkm)
 export(fpm)
 export(getBestQ)
@@ -27,6 +29,7 @@ export(padj)
 export(plotAberrantPerSample)
 export(plotCountCorHeatmap)
 export(plotCountGeneSampleHeatmap)
+export(plotDispEsts)
 export(plotEncDimSearch)
 export(plotExpectedVsObservedCounts)
 export(plotExpressedGenes)
@@ -41,14 +44,21 @@ export(sampleExclusionMask)
 export(sizeFactors)
 export(theta)
 export(zScore)
+exportMethods(aberrant)
 exportMethods(computePvalues)
 exportMethods(computeZscores)
+exportMethods(dispersions)
 exportMethods(filterExpression)
-exportMethods(fit)
+exportMethods(plotAberrantPerSample)
+exportMethods(plotCountCorHeatmap)
 exportMethods(plotDispEsts)
+exportMethods(plotEncDimSearch)
+exportMethods(plotQQ)
+exportMethods(plotVolcano)
 exportMethods(results)
 import(data.table, except=melt)
 
+import(methods)
 importFrom(BBmisc,chunk)
 importFrom(BBmisc,isFALSE)
 importFrom(BBmisc,isScalarCharacter)
@@ -58,7 +68,6 @@ importFrom(BBmisc,isScalarNumeric)
 importFrom(BBmisc,isScalarValue)
 importFrom(BBmisc,seq_col)
 importFrom(BBmisc,seq_row)
-importFrom(Biobase,rowMax)
 importFrom(BiocGenerics,estimateSizeFactors)
 importFrom(BiocGenerics,plotDispEsts)
 importFrom(BiocParallel,SerialParam)
@@ -79,6 +88,7 @@ importFrom(DESeq2,fpkm)
 importFrom(DESeq2,fpm)
 importFrom(DESeq2,makeExampleDESeqDataSet)
 importFrom(DESeq2,normalizationFactors)
+importFrom(DESeq2,plotDispEsts)
 importFrom(DESeq2,replaceOutliers)
 importFrom(DESeq2,show)
 importFrom(DESeq2,sizeFactors)
@@ -90,7 +100,6 @@ importFrom(GenomicRanges,width)
 importFrom(IRanges,IRanges)
 importFrom(PRROC,pr.curve)
 importFrom(RColorBrewer,brewer.pal)
-importFrom(Rcpp,sourceCpp)
 importFrom(S4Vectors,"metadata<-")
 importFrom(S4Vectors,DataFrame)
 importFrom(S4Vectors,metadata)
@@ -105,7 +114,7 @@ importFrom(SummarizedExperiment,assays)
 importFrom(SummarizedExperiment,colData)
 importFrom(SummarizedExperiment,mcols)
 importFrom(SummarizedExperiment,rowData)
-importFrom(compiler,cmpfun)
+importFrom(generics,fit)
 importFrom(ggplot2,aes)
 importFrom(ggplot2,annotate)
 importFrom(ggplot2,element_blank)
@@ -134,9 +143,6 @@ importFrom(ggplot2,theme_bw)
 importFrom(ggplot2,xlab)
 importFrom(ggplot2,ylab)
 importFrom(ggplot2,ylim)
-importFrom(gplots,barplot2)
-importFrom(gplots,bluered)
-importFrom(gplots,heatmap.2)
 importFrom(grDevices,colorRampPalette)
 importFrom(graphics,abline)
 importFrom(graphics,axis)
@@ -157,10 +163,6 @@ importFrom(matrixStats,rowMeans2)
 importFrom(matrixStats,rowMedians)
 importFrom(matrixStats,rowQuantiles)
 importFrom(matrixStats,rowSds)
-importFrom(methods,as)
-importFrom(methods,is)
-importFrom(methods,new)
-importFrom(methods,validObject)
 importFrom(pcaMethods,loadings)
 importFrom(pcaMethods,pca)
 importFrom(pheatmap,pheatmap)

NEWS

@@ -1,3 +1,9 @@
+CHANGES IN VERSION 1.7.1
+-----------------------------
+    o Move to S3/S4 methods to be compatible with FRASER
+    o Due to the S3/S4 changes minor changes in the argument names happend 
+      mainly ods -> object or x
+
 CHANGES IN VERSION 1.3.5
 -----------------------------
     o Change plotAberrantPerSample from base-R to ggplot2

R/AllGenerics.R

@@ -0,0 +1,50 @@
+#' @rdname aberrant
+#' @export
+setGeneric("aberrant", function(object, ...) standardGeneric("aberrant"))
+
+#' @importFrom DESeq2 dispersions
+#' @noRd
+#' @export
+DESeq2::dispersions
+
+#' @rdname filterExpression
+#' @export
+setGeneric("filterExpression", function(object, ...)
+        standardGeneric("filterExpression"))
+
+#' @importFrom generics fit
+#' @noRd
+#' @export
+generics::fit
+
+#' @rdname plotFunctions
+#' @export
+setGeneric("plotAberrantPerSample", function(object, ...)
+        standardGeneric("plotAberrantPerSample"))
+
+#' @rdname plotFunctions
+#' @export
+setGeneric("plotCountCorHeatmap", function(object, ...) 
+        standardGeneric("plotCountCorHeatmap"))
+
+#' @importFrom DESeq2 plotDispEsts
+#' @noRd
+#' @export
+DESeq2::plotDispEsts
+
+#' @rdname plotFunctions
+#' @export
+setGeneric("plotEncDimSearch", function(object, ...)
+        standardGeneric("plotEncDimSearch"))
+
+#' @rdname plotFunctions
+#' @export
+setGeneric("plotQQ", function(object, ...) standardGeneric("plotQQ"))
+
+#' @rdname plotFunctions
+#' @export
+setGeneric("plotVolcano", function(object, ...) standardGeneric("plotVolcano"))
+
+#' @rdname results
+#' @export
+setGeneric("results", function(object, ...) standardGeneric("results"))

R/filterExpression.R

@@ -1,3 +1,19 @@
+filterExpression.OUTRIDER <- function(object, gtfFile, fpkmCutoff=1, 
+                    percentile=0.95, filterGenes=TRUE, savefpkm=FALSE, 
+                    minCounts=FALSE, addExpressedGenes=TRUE, ...){
+    object <- filterMinCounts(object, filterGenes=filterGenes, 
+            verbose=minCounts)
+    if(isTRUE(minCounts)){
+        return(object)
+    }
+    if(!missing(gtfFile)){
+        object <- computeGeneLength(object, gtfFile=gtfFile, ...)
+    }
+    filterExp(object, fpkmCutoff=fpkmCutoff, percentile=percentile,
+            filterGenes=filterGenes, savefpkm=savefpkm, 
+            addExpressedGenes=addExpressedGenes)
+}
+
 #' 
 #' Filter expression
 #' 
@@ -8,7 +24,7 @@
 #' the basepair parameter as described in \code{\link[DESeq2]{fpkm}}.
 #' 
 #' @rdname filterExpression
-#' @param x An OutriderDataSet object
+#' @param object An OutriderDataSet object
 #' @param filterGenes If TRUE, the default, the object is subseted.
 #' @param minCounts If TRUE, only genes with 0 counts in all samples are 
 #'             filtered
@@ -39,26 +55,6 @@
 #' dim(ods)
 #' 
 #' @export
-setGeneric("filterExpression", 
-        function(x, ...) standardGeneric("filterExpression"))
-
-filterExpression.OUTRIDER <- function(x, gtfFile, fpkmCutoff=1, 
-                    percentile=0.95, filterGenes=TRUE, savefpkm=FALSE, 
-                    minCounts=FALSE, addExpressedGenes=TRUE, ...){
-    x <- filterMinCounts(x, filterGenes=filterGenes, verbose=minCounts)
-    if(isTRUE(minCounts)){
-        return(x)
-    }
-    if(!missing(gtfFile)){
-        x <- computeGeneLength(x, gtfFile=gtfFile, ...)
-    }
-    filterExp(x, fpkmCutoff=fpkmCutoff, percentile=percentile,
-            filterGenes=filterGenes, savefpkm=savefpkm, 
-            addExpressedGenes=addExpressedGenes)
-}
-
-#' @rdname filterExpression
-#' @export
 setMethod("filterExpression", "OutriderDataSet", filterExpression.OUTRIDER)
 
 filterExp <- function(ods, fpkmCutoff, percentile, filterGenes, savefpkm, 

R/fitNB.R

@@ -7,14 +7,12 @@
 #' 
 #' @param object An OutriderDataSet
 #' @param BPPARAM by default bpparam()
-#' @param ... additional arguments, currently not used.
+#' @param ... Currently not used.
 #' @return An OutriderDataSet object with the fitted model. Accessible through:
 #'             \code{mcols(ods)[,c('mu', 'theta')]}.
 #' 
-#' @docType methods
 #' @name fit
 #' @rdname fit
-#' @aliases fit fit,OutriderDataSet-method
 #' 
 #' @examples 
 #' ods <- makeExampleOutriderDataSet()
@@ -23,13 +21,15 @@
 #' 
 #' mcols(ods)[1:10,c('mu', 'theta')]
 #' 
-#' @exportMethod fit 
-setGeneric("fit", function(object, ...) standardGeneric("fit"))
-
-#' @rdname fit
 #' @export
-setMethod("fit", "OutriderDataSet", function(object, BPPARAM=bpparam()){
-    fitTheta(object, BPPARAM=BPPARAM)})
+fit.OutriderDataSet <- function(object, BPPARAM=bpparam(), ...){
+    if(length(list(...))){
+        stop("... is currently not used. Please remove the ", 
+             "additional arguments: ", 
+             paste(names(list(...)), collapse=", "))
+    }
+    fitTheta(object, BPPARAM=BPPARAM)
+}
 
 fitTheta <- function(ods, BPPARAM){
     checkOutriderDataSet(ods)

R/getNSetterFuns.R

@@ -73,11 +73,15 @@ padj <- function(ods){
     return(ods)
 }
 
+
 #' @rdname getter_setter_functions
-#' @export dispersions
-setMethod("dispersions", signature(object="OutriderDataSet"), 
+#' @aliases dispersions dispersions,OutriderDataSet-method
+#' @seealso \code{\link[DESeq2]{estimateDispersions}}
+#' @export
+setMethod("dispersions", signature(object="OutriderDataSet"),
     function(object, ...){ 1/theta(object) })
 
+
 #' @rdname getter_setter_functions
 #' @export theta
 theta <- function(ods){

R/method-evaluation.R

@@ -1,15 +1,32 @@
+aberrant.OUTRIDER <- function(object, padjCutoff=0.05, zScoreCutoff=0, 
+                    by=c("none", "sample", "gene")){
+    checkFullAnalysis(object)
+
+    aberrantEvents <- padj(object) <= padjCutoff
+    if(isScalarNumeric(zScoreCutoff, na.ok=FALSE)){
+        aberrantEvents <- aberrantEvents & abs(zScore(object)) >= zScoreCutoff
+    }
+
+    return(switch(match.arg(by),
+            none = aberrantEvents,
+            sample = colSums(aberrantEvents, na.rm=TRUE),
+            gene = rowSums(aberrantEvents, na.rm=TRUE)
+    ))
+}
+
 #' 
 #' Number of aberrant events
 #' 
 #' Identifies the aberrant events and returns the number of aberrant counts per
 #' gene or sample or returns a matrix indicating aberrant events.
 #' 
-#' @param ods An OutriderDataSet object
+#' @param object An OutriderDataSet object
 #' @param padjCutoff The padjust cutoff 
 #' @param zScoreCutoff The absolute Z-score cutoff, 
 #'             if NA or NULL no Z-score cutoff is used
 #' @param by if the results should be summarized by 'sample', 
 #'             'gene' or not at all (default).
+#' @param ... Currently not in use.
 #'
 #' @return The number of aberrent events by gene or sample or a TRUE/FALSE 
 #'             matrix of the size sample x gene of aberrent events.
@@ -24,19 +41,4 @@
 #' 
 #' @rdname aberrant
 #' @export
-aberrant <- function(ods, padjCutoff=0.05, zScoreCutoff=0, 
-                    by=c("none", "sample", "gene")){
-    checkFullAnalysis(ods)
-
-    aberrantEvents <- padj(ods) <= padjCutoff
-    if(isScalarNumeric(zScoreCutoff, na.ok=FALSE)){
-        aberrantEvents <- aberrantEvents & abs(zScore(ods)) >= zScoreCutoff
-    }
-
-    return(switch(match.arg(by),
-            none = aberrantEvents,
-            sample = colSums(aberrantEvents, na.rm=TRUE),
-            gene = rowSums(aberrantEvents, na.rm=TRUE)
-    ))
-}
-
+setMethod("aberrant", signature="OutriderDataSet", aberrant.OUTRIDER)