Renamed SE saving options to align with alabaster.base's docs.

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: alabaster.se
 Title: Load and Save SummarizedExperiments from File
-Version: 1.3.3
-Date: 2023-12-12
+Version: 1.3.4
+Date: 2024-02-21
 Authors@R: person("Aaron", "Lun", role=c("aut", "cre"), email="[email protected]")
 License: MIT + file LICENSE
 Description: 
@@ -27,7 +27,7 @@ Suggests:
     testthat,
     BiocStyle
 VignetteBuilder: knitr
-RoxygenNote: 7.2.3
+RoxygenNote: 7.3.1
 biocViews:
     DataImport,
     DataRepresentation

R/saveSummarizedExperiment.R

@@ -4,7 +4,7 @@
 #' 
 #' @param x A \linkS4class{SummarizedExperiment} object or one of its subclasses.
 #' @inheritParams alabaster.base::saveObject
-#' @param summarizedexperiment.allow.dataframe.assay Logical scalar indicating whether to allow data frames as assays of \code{x}.
+#' @param SummarizedExperiment.allow.dataframe.assay Logical scalar indicating whether to allow data frames as assays of \code{x}.
 #' @param ... Further arguments to pass to internal \code{\link{altSaveObject}} calls.
 #'
 #' @return \code{x} is saved into \code{path} and \code{NULL} is invisibly returned.
@@ -44,15 +44,15 @@ NULL
 #' @importFrom jsonlite toJSON
 #' @import alabaster.base
 #' @import methods
-setMethod("saveObject", "SummarizedExperiment", function(x, path, summarizedexperiment.allow.dataframe.assay=FALSE, ...) {
+setMethod("saveObject", "SummarizedExperiment", function(x, path, SummarizedExperiment.allow.dataframe.assay=FALSE, ...) {
     dir.create(path)
     saveObjectFile(
         path, 
         "summarized_experiment", 
         list(summarized_experiment=list(version="1.0", dimensions=dim(x)))
     )
 
-    args <- list(summarizedexperiment.allow.dataframe.assay=summarizedexperiment.allow.dataframe.assay, ...)
+    args <- list(SummarizedExperiment.allow.dataframe.assay=SummarizedExperiment.allow.dataframe.assay, ...)
 
     cd <- colData(x)
     empty.cd <- make_zero_col_DFrame(nrow(cd))
@@ -94,7 +94,7 @@ setMethod("saveObject", "SummarizedExperiment", function(x, path, summarizedexpe
             aname <- as.character(i - 1L)
             curmat <- all.assays[[i]]
 
-            if (is.data.frame(curmat) || (is(curmat, "DataFrame") && !summarizedexperiment.allow.dataframe.assay)) {
+            if (is.data.frame(curmat) || (is(curmat, "DataFrame") && !SummarizedExperiment.allow.dataframe.assay)) {
                 stop("assays should not contain data frames, see ?'saveObject,SummarizedExperiment-method'")
             }
 

tests/testthat/test-SummarizedExperiment.R

@@ -250,7 +250,7 @@ test_that("stageObject handles data frames in the assays", {
     expect_error(saveObject(se, tmp), "should not contain data frames")
 
     tmp <- tempfile()
-    saveObject(se2, tmp, summarizedexperiment.allow.dataframe.assay=TRUE)
+    saveObject(se2, tmp, SummarizedExperiment.allow.dataframe.assay=TRUE)
     out2 <- readObject(tmp)
     expect_identical(assay(se2), assay(out2))
 })