johannes fixes

rformassspectrometry · Sep 19, 2024 · c2c055c · c2c055c
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diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: MsIO
 Title: Serializing and restoring/importing mass spectrometry data objects
-Version: 0.0.4
+Version: 0.0.5
 Authors@R:
     c(person(given = "Johannes", family = "Rainer",
              email = "Johannes.Rainer@eurac.edu",

diff --git a/R/MetaboLightsParam.R b/R/MetaboLightsParam.R
@@ -13,29 +13,30 @@
 #' MetaboLights database (https://www.ebi.ac.uk/metabolights/index) by
 #' providing its unique study `mtblsId`. This function is particularly useful
 #' for importing metabolomics data into an `MsExperiment` object for further
-#' analysis in the R environment. It is important to note that this method
-#' can *only* be used for importing into an R environment via `readMsObject()`.
-#' It cannot be used with the `saveMsObject()` method.
+#' analysis in the R environment.
+#' It is important to note that at present it is only possible to *read*
+#' (import) data from MetaboLights, but not to *save* data to MetaboLights.
 #'
 #' If the study contains multiple assays, the user will be prompted to select
 #' which assay to load. The resulting `MsExperiment` object will include a
 #' `sampleData` slot populated with data extracted from the selected assay.
 #'
 #' Users can define how to filter this `sampleData` table by specifying a few
 #' parameters. The `keepOntology` parameter is set to `TRUE` by default, meaning
-#' that all columns related to ontology are retained. If set to `FALSE`, they are
+#' that all ontology-related columns are retained. If set to `FALSE`, they are
 #' removed. If ontology columns are kept, some column names may be duplicated and
 #' therefore numbered. The order of these columns is important, as it reflects the
 #' assay and sample information available in MetaboLights.
 #'
 #' The `keepProtocol` parameter is also set to `TRUE` by default, meaning that
 #' all columns related to protocols are kept. If set to `FALSE`, they are removed.
-#' The `simplify` parameter, defaulted to `TRUE`, means that columns filled with
-#' NAs or duplicated content will be removed. In the case of duplicated content,
-#' only the first occurring column will be retained.
+#' The `simplify` parameter (default `simplify = TRUE`) allows to define
+#' whether duplicated columns or columns containing only missing values should
+#' be removed. In the case of duplicated content, only the first occurring
+#' column will be retained.
 #'
-#' Further filtering can be performed using the `filePattern` slot of the
-#' `MetaboLightsParam` object. The default for this slot is
+#' Further filtering can be performed using the `filePattern` parameter of the
+#' `MetaboLightsParam` object. The default for this parameter is
 #' `"mzML$|CDF$|cdf$|mzXML$"`, which corresponds to the supported raw data file
 #' types.
 #'
@@ -53,23 +54,23 @@
 #' types.
 #'
 #' @param keepOntology `logical(1)` Whether to keep columns related to ontology
-#' in the `sampleData` slot. Default is `TRUE`.
+#' in the `sampleData` parameter. Default is `TRUE`.
 #'
 #' @param keepProtocol `logical(1)` Whether to keep columns related to protocols
-#' information in the `sampleData` slot. Default is `TRUE`.
+#' information in the `sampleData` parameter. Default is `TRUE`.
 #'
 #' @param simplify `logical(1)` Whether to simplify the `sampleData` table by
 #' removing columns filled with NAs or duplicated content. Default is `TRUE`.
 #'
 #' @inheritParams saveMsObject
 #'
-#' @returns An `MsExperiment` object with the `sampleData` slot populated using
+#' @returns An `MsExperiment` object with the `sampleData` parameter populated using
 #' MetaboLights sample and assay information. The spectra data is represented
 #' as a `MsBackendMetabolights` object, generated from the raw data files
 #' associated with the selected assay of the specified MetaboLights ID
 #' (`mtblsId`).
 #'
-#' @author Philippine Louail,Johannes Rainer
+#' @author Philippine Louail
 #'
 #' @importFrom methods new
 #'

diff --git a/R/MsExperiment.R b/R/MsExperiment.R
@@ -225,17 +225,21 @@ setMethod("readMsObject",
 
               ## Extract and read assay files
               assays <- all_fls[grepl("^a_", all_fls)]
-              if (length(param@assayName) > 0) selected_assay <- param@assayName
-              else if (length(assays) > 1 && length(param@assayName) == 0) {
-                  cat("Multiple assay files found:\n")
-                  selection <- menu(assays,
-                                    title = paste("Please choose the assay",
-                                    "file you want to use:"))
-                  selected_assay <- assays[selection]
-              } else if (length(assays) == 1) {
-                  selected_assay <- assays
-                  cat("Only one assay file found:", selected_assay, "\n")
+              if (length(param@assayName) > 0)
+                  selected_assay <- param@assayName
+              else {
+                  if (length(assays) == 1) {
+                      selected_assay <- assays
+                      message("Only one assay file found:", selected_assay, "\n")
+                  } else {
+                      message("Multiple assay files found:\n")
+                      selection <- menu(assays,
+                                        title = paste("Please choose the assay",
+                                                      "file you want to use:"))
+                      selected_assay <- assays[selection]
+                  }
               }
+
               assay_data <- read.table(paste0(pth, selected_assay),
                                        header = TRUE, sep = "\t",
                                        check.names = FALSE)
@@ -267,8 +271,8 @@ setMethod("readMsObject",
               nme <- colnames(merged_data)[which(merged_data[1, ] == fl)]
               merged_data <- merged_data[grepl(param@filePattern,
                                                merged_data[, nme]), ]
-
-              object@sampleData <- DataFrame(merged_data)
+              nme <- gsub(" ", "_", nme) #use concatenate instead ?
+              object@sampleData <- DataFrame(merged_data, check.names = FALSE)
               object <- MsExperiment::linkSampleData(object,
                                                      with = paste0("sampleData.",
                                                                 nme,

diff --git a/man/MetaboLightsParam.Rd b/man/MetaboLightsParam.Rd
diff --git a/vignettes/MsIO.Rmd b/vignettes/MsIO.Rmd
@@ -250,7 +250,6 @@ annotation information as a `DataFrame` from the *sample_data* subfolder:
 readObject(path = file.path(d, "sample_data"))
 ```
 
-# Loading data from *MetaboLights*
 
 # Loading data from *MetaboLights*