Pass delayed and fill to combineCols() of altExps (#68)

This ensures that the treatment of the alternative experiment's assays
is consistent with that of the main experiment.

Identified in LTLA/mumosa#5 (comment)

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: SingleCellExperiment
-Version: 1.20.0
-Date: 2022-08-29
+Version: 1.20.1
+Date: 2023-03-15
 Title: S4 Classes for Single Cell Data
 Authors@R: c(
         person("Aaron", "Lun", role=c("aut", "cph"), email="[email protected]"),

R/combine.R

@@ -308,7 +308,7 @@ setMethod("combineCols", "SingleCellExperiment", function(x, ..., delayed=TRUE,
         }
 
         tryCatch({
-            new.altexps[[i]] <- SummarizedExperimentByColumn(do.call(combineCols, c(collated, list(use.names=use.names))))
+            new.altexps[[i]] <- SummarizedExperimentByColumn(do.call(combineCols, c(collated, list(use.names=use.names, delayed=delayed, fill=fill))))
         }, error=function(e) {
             warning("failed to combine '", i, "' in 'altExps(<", class(ans), ">)':\n  ", conditionMessage(e))
         })

tests/testthat/test-sce-combine.R

@@ -105,3 +105,35 @@ test_that("cbind handles errors in the internal fields correctly", {
     sce4 <- rbind(A=sce, B=sce) 
     expect_identical(objectVersion(sce4), objectVersion(sce))
 })
+
+test_that("combineCols passes on delay when combining altExps", {
+    sce.combined <- combineCols(sce, sce, use.names=FALSE, delayed=FALSE)
+    expect_is(assay(altExp(sce.combined)), "matrix")
+
+    sce.combined2 <- combineCols(sce, sce, use.names=FALSE, delayed=TRUE)
+    expect_is(assay(altExp(sce.combined2)), "DelayedMatrix")
+})
+
+test_that("combineCols passes on fill when combining altExps", {
+    sce1 <- sce[1:6, 1:10]
+    rownames(sce1) <- LETTERS[seq_len(nrow(sce1))]
+    colnames(sce1) <- letters[seq_len(ncol(sce1))]
+    altExp(sce1) <- altExp(sce1)[1:6, ]
+
+    sce2 <- sce[1:14, 11:20]
+    rownames(sce2) <- LETTERS[1:14]
+    colnames(sce2) <- letters[seq_len(ncol(sce2)) + ncol(sce1)]
+    altExp(sce2) <- altExp(sce2)[4:7, ]
+
+    sce.combined1 <- combineCols(sce1, sce2, use.names=TRUE)
+    expect_true(anyNA(assay(sce.combined1)))
+
+    sce.combined2 <- combineCols(sce1, sce2, use.names=TRUE, fill = -1)
+    expect_true(any(assay(sce.combined2) == -1))
+
+    sce.combined3 <- combineCols(sce1, sce2, use.names=TRUE)
+    expect_true(anyNA(assay(altExp(sce.combined3))))
+
+    sce.combined4 <- combineCols(sce1, sce2, use.names=TRUE, fill = -1)
+    expect_true(any(assay(sce.combined4) == -1))
+})