1. bsseq
  2. R
  3. hdf5_utils.R
Browse code

Accomodate for change to class(matrix()) in R 4.0

Hervé Pagès authored on 24/03/2020 07:29:35
Showing 1 changed files
R/hdf5_utils.R
History View file @ 56e4d81
... ... 
@@ -17,7 +17,9 @@
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         return(.getSeedClasses(seed))
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     }
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     else {
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-        class(seed)
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+        # Pick the first element returned by class() (starting with R 4.0,
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+        # 'class(matrix())' is 'c("matrix", "array")').
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+        class(seed)[[1L]]
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     }
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 }
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Browse code

Re-sync with DelayedArray

Peter Hickey authored on 08/04/2018 18:47:50
Showing 1 changed files
R/hdf5_utils.R
History View file @ be836cb
... ... 
@@ -4,8 +4,12 @@
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 #
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 .getSeedClasses <- function(seed) {
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-    if (is(seed, "SeedBinder") || is(seed, "ConformableSeedCombiner")) {
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-        seeds <- seed@seeds
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+    if (is(seed, "DelayedOp")) {
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+        seeds <- try(seed@seeds, silent = TRUE)
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+        if (is(seeds, "try-error")) {
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+            seed <- seed@seed
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+            return(.getSeedClasses(seed))
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+        }
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         return(lapply(seeds, .getSeedClasses))
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     } else if (is(seed, "DelayedArray")) {
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         # A DelayedArray can have another DelayedArray as a seed
Browse code

bsseq now uses DelayedMatrix objects from the DelayedArray package for all matrix-like data

Peter Hickey authored on 07/04/2017 17:42:29
Showing 1 changed files
R/hdf5_utils.R
History View file @ 95e9059
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new file mode 100644
... ... 
@@ -0,0 +1,42 @@
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+#-------------------------------------------------------------------------------
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+# Is a DelayedMatrix object (or the assays of a SummarizedExperiment object)
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+# backed by a HDF5 file?
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+#
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+
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+.getSeedClasses <- function(seed) {
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+    if (is(seed, "SeedBinder") || is(seed, "ConformableSeedCombiner")) {
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+        seeds <- seed@seeds
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+        return(lapply(seeds, .getSeedClasses))
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+    } else if (is(seed, "DelayedArray")) {
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+        # A DelayedArray can have another DelayedArray as a seed
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+        seed <- seed@seed
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+        return(.getSeedClasses(seed))
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+    }
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+    else {
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+        class(seed)
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+    }
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+}
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+
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+# NOTE: Returns TRUE if *any* assay is HDF5Array-backed and FALSE if *all*
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+#       assays are not HDF5Array-backed
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+.isHDF5ArrayBacked <- function(object) {
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+    if (is(object, "SummarizedExperiment")) {
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+        return(all(vapply(X = assays(object, withDimnames = FALSE),
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+                          FUN = .isHDF5ArrayBacked,
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+                          FUN.VALUE = logical(1L))))
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+    }
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+    if (is(object, "DelayedArray")) {
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+        seed <- object@seed
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+        seed_classes <- .getSeedClasses(seed)
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+        is_hdf5_backed <- vapply(unlist(seed_classes, use.names = FALSE),
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+                                 extends, class2 = "HDF5ArraySeed",
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+                                 logical(1L))
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+        return(any(is_hdf5_backed))
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+    } else if (is.matrix(object)) {
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+        FALSE
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+    } else if (is.null(object)) {
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+        FALSE
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+    } else {
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+        stop("Don't know how to handle object of class ", class(object))
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+    }
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+}