Merge with master

.github/workflows/check-bioc.yml

@@ -52,10 +52,11 @@ jobs:
       fail-fast: false
       matrix:
         config:
-          - { os: ubuntu-latest, r: '4.2', bioc: '3.16', cont: "bioconductor/bioconductor_docker:RELEASE_3_16", rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest" }
-          - { os: ubuntu-latest, r: 'next', bioc: '3.17', cont: "bioconductor/bioconductor_docker:RELEASE_3_17", rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest" }
-          - { os: macOS-latest, r: '4.2', bioc: '3.16'}
-          - { os: windows-latest, r: '4.2', bioc: '3.16'}
+          # This needs to be updated after each Bioconductor release. Please make sure we have the matching R and Bioc versions in it. 
+          - { os: ubuntu-latest, r: '4.3', bioc: '3.18', cont: "bioconductor/bioconductor_docker:RELEASE_3_18", rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest" }
+          - { os: ubuntu-latest, r: 'next', bioc: '3.19', cont: "bioconductor/bioconductor_docker:devel", rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest" }
+          - { os: macOS-latest, r: '4.3', bioc: '3.18'}
+          - { os: windows-latest, r: '4.3', bioc: '3.18'}
           ## Check https://github.com/r-lib/actions/tree/master/examples
           ## for examples using the http-user-agent
     env:
@@ -249,7 +250,7 @@ jobs:
           rcmdcheck::rcmdcheck(
               args = c("--no-manual", "--no-vignettes", "--timings"),
               build_args = c("--no-manual", "--keep-empty-dirs", "--no-resave-data"),
-              error_on = "error",
+              error_on = "warning",
               check_dir = "check"
           )
         shell: Rscript {0}
@@ -313,7 +314,7 @@ jobs:
         if: failure()
         uses: actions/upload-artifact@master
         with:
-          name: ${{ runner.os }}-biocversion-RELEASE_3_16-r-4.2-results
+          name: ${{ runner.os }}-biocversion-RELEASE_3_18-r-4.3-results
           path: check
 
         ## Note that DOCKER_PASSWORD is really a token for your dockerhub

DESCRIPTION

@@ -2,14 +2,17 @@ Package: FRASER
 Type: Package
 Title: Find RAre Splicing Events in RNA-Seq Data
 Version: 1.99.3
-Date: 2022-11-25
+Date: 2024-02-11
 Authors@R: c(
     person("Christian", "Mertes", role=c("aut", "cre"), 
-            email="mertes@in.tum.de"),
-    person("Ines", "Scheller",  role=c("aut"), email="scheller@in.tum.de"),
-    person("Karoline", "Lutz", role=c("aut")),
-    person("Vicente", "Yepez", role=c("ctb"), email="yepez@in.tum.de"),
-    person("Julien", "Gagneur", role=c("aut"), email="gagneur@in.tum.de"))
+            email="mertes@in.tum.de", comment=c(ORCID="0000-0002-1091-205X")),
+    person("Ines", "Scheller", role=c("aut"), email="scheller@in.tum.de",
+            comment=c(ORCID="0000-0003-4533-7857")),
+    person("Karoline", "Lutz", role=c("ctb"), email="lutzk@in.tum.de"),
+    person("Vicente", "Yepez", role=c("aut"), email="yepez@in.tum.de",
+            comment=c(ORCID="0000-0001-7916-3643")),
+    person("Julien", "Gagneur", role=c("aut"), email="gagneur@in.tum.de",
+            comment=c(ORCID="0000-0002-8924-8365")))
 Description: Detection of rare aberrant splicing events in transcriptome 
     profiles. Read count ratio expectations are modeled by an autoencoder to
     control for confounding factors in the data. Given these expectations, 
@@ -28,8 +31,8 @@ biocViews:
     Coverage
 License: MIT + file LICENSE
 URL: https://github.com/gagneurlab/FRASER
-BugRepots: https://github.com/gagneurlab/FRASER/issues
-RoxygenNote: 7.2.3
+BugReports: https://github.com/gagneurlab/FRASER/issues
+RoxygenNote: 7.3.1
 Encoding: UTF-8
 VignetteBuilder: knitr
 Depends:
@@ -75,7 +78,8 @@ Imports:
     tools,
     utils,
     VGAM
-Suggests: 
+Suggests:
+    magick,
     BiocStyle,
     knitr,
     rmarkdown,

R/AllGenerics.R

@@ -234,8 +234,11 @@ setReplaceMethod("nonSplicedReads", "FraserDataSet", function(object, value){
 #' @param x A \code{FraserDataSet} object
 #' @param i A integer vector to subset the rows/ranges
 #' @param j A integer vector to subset the columns/samples
-#' @param by a character (j or ss) definig if we subset by
+#' @param by a character (j or ss) defining if we subset by
 #'             junctions or splice sites
+#' @param ... Parameters currently not used or passed on
+#' @param drop No dimension reduction is done. And the \code{drop}
+#'             parameter is currently not used at all.
 #' @return A subsetted \code{FraserDataSet} object
 #' @examples
 #'     fds <- createTestFraserDataSet()
@@ -244,7 +247,7 @@ setReplaceMethod("nonSplicedReads", "FraserDataSet", function(object, value){
 #'     fds[1:10,by="ss"]
 #'
 #' @rdname subset
-subset.FRASER <- function(x, i, j, by=c("j", "ss")){
+subset.FRASER <- function(x, i, j, by=c("j", "ss"), ..., drop=FALSE){
     if(length(by) == 1){
         by <- whichReadType(x, by)
     }
@@ -292,14 +295,14 @@ subset.FRASER <- function(x, i, j, by=c("j", "ss")){
         idxNSR <- rowData(x, type="ss")[['spliceSiteID']] %in% ssIdx
 
         # subset it
-        nsrObj <- nsrObj[idxNSR,j]
+        nsrObj <- nsrObj[idxNSR,j,drop=FALSE]
     }
 
     # subset the inheritate SE object
     if(length(x) == 0){
         i <- NULL
     }
-    subX <- as(as(x, "RangedSummarizedExperiment")[i,j], "FraserDataSet")
+    subX <- as(as(x, "RangedSummarizedExperiment")[i,j,drop=FALSE], "FraserDataSet")
 
     # create new FraserDataSet object
     newx <- new("FraserDataSet",
@@ -315,7 +318,7 @@ subset.FRASER <- function(x, i, j, by=c("j", "ss")){
 }
 #' @rdname subset
 #' @export
-setMethod("[", c("FraserDataSet", "ANY", "ANY"), subset.FRASER)
+setMethod("[", c("FraserDataSet", "ANY", "ANY", drop="ANY"), subset.FRASER)
 
 
 #'

src/Makevars

@@ -1,4 +1,2 @@
-CXX_STD = CXX11
-
 PKG_CXXFLAGS = $(SHLIB_OPENMP_CXXFLAGS) -DARMA_DONT_USE_OPENMP
 PKG_LIBS = $(SHLIB_OPENMP_CXXFLAGS) $(LAPACK_LIBS) $(BLAS_LIBS) $(FLIBS)

src/Makevars.win

@@ -1,4 +1,2 @@
-CXX_STD = CXX11
-
 PKG_CXXFLAGS = $(SHLIB_OPENMP_CXXFLAGS) -DARMA_DONT_USE_OPENMP
 PKG_LIBS = $(SHLIB_OPENMP_CXXFLAGS) $(LAPACK_LIBS) $(BLAS_LIBS) $(FLIBS)

tests/testthat/test_getter_setter.R

@@ -12,3 +12,12 @@ test_that("counts", {
     expect_equal(counts(fds, type="theta", side='other'),
             N(fds, "theta") - K(fds, "theta"))
 })
+
+test_that("generic functions", {
+    # test that the correct functions are selected and called
+    methDef <- selectMethod("[", c("FraserDataSet", "ANY", "ANY", drop="ANY"))
+    expect_equal(slot(methDef, "defined")[["x"]], "FraserDataSet")
+    methDef <- selectMethod("[", 
+            c("FraserDataSet", "ANY", "ANY", drop="missing"))
+    expect_equal(slot(methDef, "defined")[["x"]], "FraserDataSet")
+})

vignettes/FRASER.Rnw

@@ -452,7 +452,7 @@ After looking at the expression distribution between filtered and unfiltered
 junctions, we can now subset the dataset:
 
 <<subset to filtered junctions, echo=TRUE>>=
-fds_filtered <- fds[mcols(fds, type="j")[,"passed"],]
+fds_filtered <- fds[mcols(fds, type="j")[,"passed"]]
 fds_filtered
 # filtered_fds not further used for this tutorial because the example dataset
 # is otherwise too small