fix all

NAMESPACE

@@ -586,3 +586,8 @@ importFrom("progress", "progress_bar")
 exportClasses("XcmsExperiment")
 exportMethods("uniqueMsLevels")
 exportMethods("filterMzRange")
+
+## saving xcms objects things
+export("RDataParam")
+exportMethods("storeResults")
+

R/AllGenerics.R

@@ -1944,7 +1944,7 @@ setGeneric("stitch.xml", function(object, lockMass) standardGeneric("stitch.xml"
 setGeneric("stitch.netCDF", function(object, lockMass) standardGeneric("stitch.netCDF"))
 setGeneric("stitch.netCDF.new", function(object, lockMass) standardGeneric("stitch.netCDF.new"))
 
-#' @title Save Xcms objects in a specified format
+#' @title Save xcms result objects in a specified format
 #'
 #' @description
 #'
@@ -1954,7 +1954,7 @@ setGeneric("stitch.netCDF.new", function(object, lockMass) standardGeneric("stit
 #'
 #' Supported `param` objects are:
 #' 
-#' - `RDataParam`: Save in an .RData format file.
+#' - [`RDataParam`]: Save in an .RData format file.
 #' 
 #' - `PlainTextParam`: Save in a plain text format (to be defined).
 #' 
@@ -1973,18 +1973,18 @@ setGeneric("stitch.netCDF.new", function(object, lockMass) standardGeneric("stit
 #'
 #' @name storeResults
 #' 
-#' @author Philippine Louail, Johannes Rainer
+#' @author Philippine Louail
 #' 
 #' @examples
 #' 
-#' ## Load a test `XcmsExperiment` object
-#' x <- 
+#' ## Load a test data set with detected peaks
+#' faahko_sub <- loadXcmsData("faahko_sub2")
 #' 
 #' ## Set up parameter to save as .RData file 
 #' param <- RDataParam(fileName = "example_xcms_results")
 #' 
 #' ## save as .RData
-#' storeResults(object = x, param = param)
+#' storeResults(object = faahko_sub, param = param)
 #' 
 #' @md
 setGeneric("storeResults", function(object, param, ...) standardGeneric("storeResults"))

R/RDataParam.R

@@ -6,9 +6,9 @@
 #'
 #' @description
 #' The `RDataParam` class and method allow users to save an `XcmsExperiment`
-#' object as an .RData file with a chosen filename. This new `param` class and
-#' method are part of the possible dispatch of the generic function
-#' `storeResults`. 
+#' object as an .RData file with a chosen filename. The object gets exported
+#' using [`save()`] function.  This `param` class and method are part of the
+#' possible dispatch of the generic function `storeResults`. 
 #' 
 #' Other available `param` classes and linked methods include:
 #'
@@ -68,3 +68,4 @@ setMethod("storeResults",
               save(object, file = param@fileName)
               }
           )
+

tests/testthat/test_XcmsExperiment.R

@@ -1322,4 +1322,7 @@ test_that("storeResults,RDataParam works", {
     expect_false(is.null(param2))
     storeResults(xmse, param = param)
     expect_true(file.exists("test"))
+    load("test")
+    expect_s4_class(object, "XcmsExperiment")
+    expect_equal(object, xmse)
 })