Fix as.DatasetExperiment() on SummarizedExperiment(data.frame(..))

Starting with SummarizedExperiment 1.23.2, the SummarizedExperiment()
constructor raises an error if one of the supplied assays has rownames
and/or colnames that don't match those inferred from the supplied 'rowData'
and 'colData' arguments. This change breaks as.DatasetExperiment()
on a SummarizedExperiment object that contains a data.frame assay
(e.g. on SummarizedExperiment(data.frame(x=1:8, y=letters[1:8]))).
This commit repairs as.DatasetExperiment() on such object.

Author: hpages

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: struct
 Type: Package
 Title: Statistics in R Using Class-based Templates
-Version: 1.5.1
+Version: 1.5.2
 Authors@R: c(
     person(
         c("Gavin","Rhys"),

R/DatasetExperiment_class.R

@@ -172,8 +172,10 @@ setMethod (f = 'as.SummarizedExperiment',
 setMethod (f = 'as.DatasetExperiment',
   signature = 'SummarizedExperiment',
   definition = function(obj) {
+    a = as.matrix(assay(obj, withDimnames=FALSE))
+    dimnames(a) = dimnames(obj)
     out=DatasetExperiment(
-      data=as.data.frame(t(assay(obj))),
+      data=as.data.frame(t(a)),
       variable_meta=as.data.frame(rowData(obj)),
       sample_meta=as.data.frame(colData(obj)),
       name=as.character(metadata(obj)$name),

tests/testthat/test-dataset.R

@@ -24,6 +24,11 @@ test_that('DatasetExperiment objects',{
 
     DE=as.DatasetExperiment(SE)
     expect_true(is(DE,'DatasetExperiment'))
+
+    SE=SummarizedExperiment(data.frame(x=1:8, y=letters[1:8]))
+    DE=as.DatasetExperiment(SE)
+    expect_true(is(DE,'DatasetExperiment'))
+    expect_identical(dimnames(DE), rev(dimnames(SE)))
 
     expect_true("name" %in% .DollarNames.struct_class(DE))