naming changes + if() fixes

DESCRIPTION

@@ -62,7 +62,7 @@ Collate:
     'MsBackendMzR.R'
     'MsExperiment.R'
     'MsExperimentFiles.R'
-    'MzTabParam.R'
     'Spectra.R'
+    'mzTabParam.R'
     'XcmsExperiment.R'
     'zzz.R'

NAMESPACE

@@ -2,8 +2,8 @@
 
 export(AlabasterParam)
 export(MetaboLightsParam)
-export(MzTabParam)
 export(PlainTextParam)
+export(mzTabParam)
 export(readObject)
 exportMethods(readMsObject)
 exportMethods(saveMsObject)

R/MzTabParam.R

@@ -1,6 +1,6 @@
 #' @title Store xcms preprocessing results to a file in mzTab-M format.
 #'
-#' @name MzTabParam
+#' @name mzTabParam
 #'
 #' @export
 #'
@@ -9,7 +9,7 @@
 #' @family MS object export and import formats.
 #'
 #' @description
-#' The `saveMsObject()` and `readMsObject()` methods with the `MzTabParam`
+#' The `saveMsObject()` and `readMsObject()` methods with the `mzTabParam`
 #' option enable users to save/load `XcmsExperiment` objects in Mz-Tab-m
 #' file format. Mainly the metadata (MTD) and Small molecule feature (SMF)
 #' tables will represent the `XcmsExperiment`. More specifically, `sampleData()`
@@ -28,7 +28,7 @@
 #' an error.
 #'
 #' @param studyId `character(1)` Will be both the `filename` of the object
-#' saved in .mztabm format and the `mzTab-ID` in the file.
+#' saved in mzTab-M format and the `mzTab-ID` in the file.
 #'
 #' @param polarity `character(1)` Describes the polarity of the experiment. Two
 #' inputs are possible, "positive" (default) or "negative".
@@ -51,7 +51,7 @@
 #'
 #' @note
 #' This function was build so that the output fit the recommendation of
-#' Mz-Tab-m file format version 2.0. These can be found here:
+#' mzTab-M file format version 2.0. These can be found here:
 #' (http://hupo-psi.github.io/mzTab/2_0-metabolomics-release/mzTab_format_specification_2_0-M_release.html)
 #'
 #' @references
@@ -75,17 +75,17 @@
 #' test_xcms <- loadXcmsData()
 #'
 #' ## Define param
-#' param <- MzTabParam(studyId = "test",
+#' param <- mzTabParam(studyId = "test",
 #'                     polarity = "positive",
 #'                     sampleDataColumn = "sample_type")
 #'
-#' ## Save as a .mzTabm file
+#' ## Save as a mzTab-M file
 #' saveMsObject(test_xcms, param)
 #'
 NULL
 
 #' @noRd
-setClass("MzTabParam",
+setClass("mzTabParam",
          slots = c(studyId = "character",
                    polarity = "character",
                    sampleDataColumn = "character",
@@ -104,29 +104,29 @@ setClass("MzTabParam",
          ),
          validity = function(object) {
              msg <- NULL
-             if(length(object@studyId) != 1)
+             if (length(object@studyId) != 1)
                  msg <- c("'studyId' has to be a character string of length 1")
-             if(length(object@polarity) != 1)
+             if (length(object@polarity) != 1)
                  msg <- c(msg, "'polarity' has to be a character string ",
                  "of length 1")
-             if(length(object@sampleDataColumn) == 0)
+             if (length(object@sampleDataColumn) == 0)
                  msg <- c(msg, "'sampleDataColumn' cannot be empty")
              if (length(object@path) != 1)
                  msg <- c(msg, "'path' has to be a character string of ",
                  "length 1")
              msg
          })
 
-#' @rdname MzTabParam
+#' @rdname mzTabParam
 #'
 #' @export
-MzTabParam <- function(studyId = character(),
+mzTabParam <- function(studyId = character(),
                        polarity = c("positive", "negative"),
                        sampleDataColumn = character(),
                        path = tempdir(),
                        optionalFeatureColumns = character(), ...) {
     polarity <- match.arg(polarity)
-    new("MzTabParam", studyId = studyId, polarity = polarity,
+    new("mzTabParam", studyId = studyId, polarity = polarity,
         sampleDataColumn = sampleDataColumn, path = path,
         optionalFeatureColumns = optionalFeatureColumns, dots = list(...))
 }

R/XcmsExperiment.R

@@ -1,4 +1,5 @@
 #' @include PlainTextParam.R
+#' @include mzTabParam.R
 #' @title Methods to save and load contents of a XcmsExperiment object
 #'
 #' @author Philippine Louail
@@ -136,7 +137,7 @@ setMethod("readMsObject",
 ################################################################################
 #' @rdname AlabasterParam
 setMethod("saveObject", "XcmsExperiment", function(x, path, ...) {
-    if(!requireNamespace("alabaster.matrix", quietly = TRUE))
+    if (!requireNamespace("alabaster.matrix", quietly = TRUE))
         stop("Required package 'alabaster.matrix' missing. Please install and ",
              "try again.", call. = FALSE)
     ## Save the MsExperiment part
@@ -190,6 +191,7 @@ setMethod("saveMsObject", signature(object = "XcmsExperiment",
                                     param = "AlabasterParam"),
           function(object, param) {
               if (file.exists(param@path))
+
                   stop("Overwriting or saving to an existing directory is not",
                        " supported. Please remove the directory defined with",
                        " parameter `path` first.")
@@ -205,19 +207,19 @@ setMethod("readMsObject", signature(object = "XcmsExperiment",
 
 ################################################################################
 ##
-## MzTabParam
+## mzTabParam
 ##
 ################################################################################
-#' @rdname MzTabParam
+#' @rdname mzTabParam
 setMethod("saveMsObject",
           signature(object = "XcmsExperiment",
-                    param = "MzTabParam"),
+                    param = "mzTabParam"),
           function(object, param){
-              if(!param@sampleDataColumn %in% colnames(object@sampleData))
+              if (!param@sampleDataColumn %in% colnames(object@sampleData))
                   stop("'sampleDataColumn' has to correspond to column names",
                        "of the sampleData() table")
-              if(length(param@optionalFeatureColumns) != 0)
-                  if(!param@optionalFeatureColumns %in% colnames(object@featureDefinitions))
+              if (length(param@optionalFeatureColumns) != 0)
+                  if (!param@optionalFeatureColumns %in% colnames(object@featureDefinitions))
                       stop("'optionalFeatureColumns' have to correspond to",
                            "column names of the featureDefinitions() table")
 

tests/testthat/test_MzTabParam.R

@@ -78,9 +78,9 @@ test_that(".mztab_study_variable_entries works", {
     expect_true(length(res2) > length(res))
 })
 
-test_that("saveMsObject,MzTabParam works", {
+test_that("saveMsObject,mzTabParam works", {
     d <- tempdir()
-    p <- MzTabParam(studyId = "test_study", path = d,
+    p <- mzTabParam(studyId = "test_study", path = d,
                     sampleDataColumn = "sample_index",
                     optionalFeatureColumns = "peakidx")
     saveMsObject(faahko, p)