subsetting by rowData, closes #228

.github/workflows/pr_check.yml

@@ -25,7 +25,12 @@ jobs:
       - name: Set Matrix Bioconductor Version
         id: set
         run: |
-          MATRIX="{\"include\":[{\"bioc_version\":\"$GITHUB_REF_NAME\"}]}"
+          if [ "${{ github.event_name }}" = "pull_request" ]; then
+            bioc_version="devel"
+          else
+            bioc_version="${GITHUB_REF_NAME}"
+          fi
+          MATRIX="{\"include\":[{\"bioc_version\":\"$bioc_version\"}]}"
           echo "matrix=$MATRIX" >> $GITHUB_OUTPUT
 
   check:
@@ -48,14 +53,14 @@ jobs:
         shell: Rscript {0}
 
       - name: Cache R packages
-        if: runner.os != 'Windows'
         uses: actions/cache@v4
         with:
           path: /usr/local/lib/R/site-library
           key: ${{ runner.os }}-r-${{ matrix.bioc_version }}-${{ hashFiles('.github/depends.Rds') }}
           restore-keys: ${{ runner.os }}-r-${{ matrix.bioc_version }}-
 
       - name: Install GPG
+        if: ${{ github.ref == 'refs/heads/devel' && github.event_name != 'pull_request' }}
         run: sudo apt-get update && sudo apt-get install -y gpg
 
       - name: Install Dependencies

DESCRIPTION

@@ -31,6 +31,7 @@ Imports:
     DelayedArray,
     GenomicRanges,
     IRanges,
+    MatrixGenerics,
     methods,
     S4Vectors,
     tidyr,

NAMESPACE

@@ -15,7 +15,9 @@ export(experiments)
 export(exportClass)
 export(getWithColData)
 export(hasAssay)
+export(hasRowData)
 export(hasRowRanges)
+export(intersectByRowData)
 export(intersectColumns)
 export(intersectRows)
 export(listToMap)
@@ -36,6 +38,7 @@ export(subsetByAssay)
 export(subsetByColData)
 export(subsetByColumn)
 export(subsetByRow)
+export(subsetByRowData)
 export(upsetSamples)
 export(wideFormat)
 exportClasses(ExperimentList)
@@ -64,7 +67,9 @@ exportMethods(dimnames)
 exportMethods(drops)
 exportMethods(experiments)
 exportMethods(exportClass)
+exportMethods(hasRowData)
 exportMethods(hasRowRanges)
+exportMethods(intersectByRowData)
 exportMethods(isEmpty)
 exportMethods(length)
 exportMethods(longForm)
@@ -79,6 +84,7 @@ exportMethods(sampleMap)
 exportMethods(show)
 exportMethods(showReplicated)
 exportMethods(splitAssays)
+exportMethods(subsetByRow)
 exportMethods(updateObject)
 import(BiocGenerics)
 import(GenomicRanges)
@@ -90,7 +96,9 @@ importFrom(BiocBaseUtils,lifeCycle)
 importFrom(BiocGenerics,colnames)
 importFrom(BiocGenerics,longForm)
 importFrom(BiocGenerics,rownames)
+importFrom(MatrixGenerics,rowRanges)
 importFrom(S4Vectors,"metadata<-")
 importFrom(S4Vectors,metadata)
+importFrom(SummarizedExperiment,rowData)
 importFrom(methods,as)
 importFrom(utils,.DollarNames)

R/MultiAssayExperiment-class.R

@@ -24,7 +24,8 @@ NULL
 #' diverse assays on a collection of specimen. Currently,  the class can handle
 #' assays that are organized instances of
 #' [`SummarizedExperiment`][SummarizedExperiment::SummarizedExperiment-class],
-#' [ExpressionSet][Biobase::ExpressionSet], `matrix`, `RaggedExperiment`
+#' \code{\link[Biobase:ExpressionSet-class]{ExpressionSet}},
+#' `matrix`, `RaggedExperiment`
 #' (inherits from [`GRangesList`][GenomicRanges::GRangesList-class]), and
 #' `RangedVcfStack`. Create new `MultiAssayExperiment` instances with the
 #' homonymous constructor, minimally with the argument [`ExperimentList`],

R/MultiAssayExperiment-helpers.R

@@ -49,6 +49,10 @@ NULL
 #'     that have a
 #'     [`rowRanges`][SummarizedExperiment::RangedSummarizedExperiment-class]
 #'     method
+#' * hasRowData: A function that identifies ExperimentList elements
+#'     that have a
+#'     [`rowData`][SummarizedExperiment::SummarizedExperiment-class]
+#'     method
 #' * getWithColData: A convenience function for extracting an assay
 #'     and associated colData
 #' * renamePrimary: A convenience function to rename the primary
@@ -363,7 +367,7 @@ setMethod("mergeReplicates", "ANY",
 #' @rdname MultiAssayExperiment-helpers
 #'
 #' @details The `longForm` "ANY" class method, works with classes such as
-#' [`ExpressionSet`][Biobase::ExpressionSet] and
+#' \code{\link[Biobase:ExpressionSet-class]{ExpressionSet}} and
 #' [`SummarizedExperiment`][SummarizedExperiment::SummarizedExperiment-class] as
 #' well as `matrix` to provide a consistent long and skinny
 #' [`DataFrame`][S4Vectors::DataFrame-class].
@@ -599,6 +603,7 @@ wideFormat <- function(object, colDataCols = NULL, check.names = TRUE,
 
 # hasRowRanges section ----------------------------------------------------
 
+#' @importFrom MatrixGenerics rowRanges
 .tryRowRanges <- function(obj) {
     res <- try(rowRanges(obj), silent = TRUE)
     if (!is(res, "try-error"))
@@ -625,6 +630,8 @@ setGeneric("hasRowRanges", function(x) standardGeneric("hasRowRanges"))
 #' @details The `hasRowRanges` method identifies assays that support
 #' a [`rowRanges`][SummarizedExperiment::RangedSummarizedExperiment-class]
 #' method _and_ return a [`GRanges`][GenomicRanges::GRanges-class] object.
+#'
+#' @exportMethod hasRowRanges
 setMethod("hasRowRanges", "MultiAssayExperiment", function(x) {
     hasRowRanges(experiments(x))
 })
@@ -635,6 +642,44 @@ setMethod("hasRowRanges", "ExperimentList", function(x) {
     vapply(x, .tryRowRanges, logical(1L))
 })
 
+# hasRowData section ------------------------------------------------------
+
+#' @importFrom SummarizedExperiment rowData
+.tryRowData <- function(obj) {
+    res <- try(rowData(obj), silent = TRUE)
+    if (!is(res, "try-error"))
+        is(res, "DataFrame")
+    else
+        FALSE
+}
+
+#' @rdname MultiAssayExperiment-helpers
+#'
+#' @aliases hasRowData
+#'
+#' @details The `hasRowData` method identifies assays that support a
+#'   [`rowData`][SummarizedExperiment::SummarizedExperiment-class] method _and_
+#'   return a [`DataFrame`][S4Vectors::DataFrame-class] object.
+#'
+#' @export
+setGeneric("hasRowData", function(x) standardGeneric("hasRowData"))
+
+#' @describeIn MultiAssayExperiment-helpers The `hasRowData` method identifies
+#'   experiments that have a `rowData` method via direct testing
+#'
+#' @exportMethod hasRowData
+setMethod("hasRowData", "MultiAssayExperiment", function(x) {
+    hasRowData(experiments(x))
+})
+
+#' @describeIn MultiAssayExperiment-helpers The `hasRowData` method identifies
+#'   experiments that have a `rowData` method via direct testing
+#'
+#' @exportMethod hasRowData
+setMethod("hasRowData", "ExperimentList", function(x) {
+    vapply(x, .tryRowData, logical(1L))
+})
+
 #' @rdname MultiAssayExperiment-helpers
 #'
 #' @param mode String indicating how `MultiAssayExperiment`

R/longFormat-deprecated.R

@@ -6,7 +6,7 @@
 #'   future release. Please use the `longForm` method instead.
 #'
 #' @details The `longFormat` "ANY" class method, works with classes such as
-#' [`ExpressionSet`][Biobase::ExpressionSet] and
+#' \code{\link[Biobase:ExpressionSet-class]{ExpressionSet}} and
 #' [`SummarizedExperiment`][SummarizedExperiment::SummarizedExperiment-class] as
 #' well as `matrix` to provide a consistent long and skinny
 #' [`DataFrame`][S4Vectors::DataFrame-class].