updates

DESCRIPTION

@@ -11,11 +11,11 @@ Authors@R: c(
     person("Vincent J", "Carey", , , c("aut", "ctb")),
     person("Levi", "Waldron", , "[email protected]", "aut"),
     person("MultiAssay", "SIG", , "[email protected]", "ctb"))
-Description: MultiAssayExperiment harmonizes data management of multiple
-    experimental assays performed on an overlapping set of specimens.  It
-    provides a familiar Bioconductor user experience by extending concepts
-    from SummarizedExperiment, supporting an open-ended mix of standard
-    data classes for individual assays, and allowing subsetting by genomic
+Description: Harmonize data management of multiple experimental assays
+    performed on an overlapping set of specimens.  It provides a familiar
+    Bioconductor user experience by extending concepts from
+    SummarizedExperiment, supporting an open-ended mix of standard data
+    classes for individual assays, and allowing subsetting by genomic
     ranges or rownames. Facilities are provided for reshaping data into
     wide and long formats for adaptability to graphing and downstream
     analysis.

R/MultiAssayExperiment-helpers.R

@@ -348,19 +348,27 @@ setMethod("mergeReplicates", "ANY",
         object <- Biobase::exprs(object)
     if (is(object, "SummarizedExperiment") || is(object, "RaggedExperiment"))
         object <- assay(object, i = i)
-    if (is(object, "matrix"))
-        object <- as.data.frame(object)
 
     ## use stats::reshape instead of reshape2::melt
     if (nullROWS)
         rownames(object) <- rowNAMES
-    object <- stats::reshape(object, idvar = "rowname",
-        ids = rownames(object), times = names(object),
-        timevar = "colname", varying = list(names(object)),
-        direction = "long", v.names = "value")
-    ## Reshape leaves rownames even if new.row.names = NULL
-    rownames(object) <- NULL
-    object[, c("rowname", "colname", "value")]
+    # if (requireNamespace("reshape2", quietly = TRUE)) {
+    if (FALSE) {
+        object <- reshape2::melt(
+            object, varnames = c("rowname", "colname"), value.name = "value"
+        )
+    } else {
+        if (is.matrix(object))
+            object <- as.data.frame(object)
+        object <- stats::reshape(object, idvar = "rowname",
+            ids = rownames(object), times = names(object),
+            timevar = "colname", varying = list(names(object)),
+            direction = "long", v.names = "value")
+        ## Reshape leaves rownames even if new.row.names = NULL
+        rownames(object) <- NULL
+        object[, c("rowname", "colname", "value")]
+    }
+    object
 }
 
 .longFormatElist <- function(object, i) {

tests/testthat/test-MultiAssayExperiment-helpers.R

@@ -238,3 +238,11 @@ test_that("renaming helpers work", {
         newaffynames
     )
 })
+
+
+test_that(".longFormatANY works", {
+    denv <- new.env(parent = emptyenv())
+    data("miniACC", package="MultiAssayExperiment", envir = denv)
+    miniACC <- denv[["miniACC"]]
+
+})