[WIP] Adding mzTab-M file import

DESCRIPTION

@@ -50,6 +50,7 @@ Imports:
     QFeatures,
     readr,
     rlang,
+    rmzTabM,
     S4Vectors,
     scales,
     shiny,
@@ -64,6 +65,8 @@ Imports:
     tools,
     utils,
     xcms
+Remotes:
+    NorStorz/rmzTabM
 Suggests:
     caret,
     FactoMineR,
@@ -77,4 +80,4 @@ VignetteBuilder:
 biocViews: Software, Visualization
 Encoding: UTF-8
 Roxygen: list(markdown = TRUE)
-RoxygenNote: 7.3.2
+RoxygenNote: 7.3.3

NAMESPACE

@@ -68,6 +68,7 @@ export(process_msp_entry)
 export(projectFromFiles)
 export(readMSDial)
 export(readMetaboscape)
+export(readMzTabM)
 export(readProjectData)
 export(readProjectFile)
 export(runMetFamily)

R/FragmentMatrixFunctions.R

@@ -1019,13 +1019,15 @@ mzClustGeneric <- function(p,
 #' @param fileSpectra path
 #' @param parameterSet list of parameters
 #' @param progress logical
+#' @param fileType optional file type/extension (e.g., "mztab", "txt") to explicitly specify format
 #'
 #' @returns resultObj
 #' @export
 convertToProjectFile <- function(filePeakMatrixPath, 
                                  fileSpectra,
                                  parameterSet, 
-                                 progress = FALSE){
+                                 progress = FALSE,
+                                 fileType = NULL){
   ## parse MS/MS spectra ----
 
   if(!is.na(progress))  if(progress)  incProgress(amount = 0.01, detail = paste("Parsing MS/MS file...", sep = "")) else print(paste("Parsing MS/MS file...", sep = ""))
@@ -1063,7 +1065,23 @@ convertToProjectFile <- function(filePeakMatrixPath,
   rm(returnObj)
 
   filePeakMatrixQF <- if(!is.null(filePeakMatrixPath)){
-    readMSDial(filePeakMatrixPath)
+    # Determine file type: use parameter if provided, default to MS-DIAL format
+    if(!is.null(fileType)) {
+      fileExtension <- tolower(fileType)
+      print(paste("Using provided fileType:", fileExtension))
+    } else {
+      fileExtension <- "other"
+      print("Defaulting to MS-DIAL format")
+    }
+
+    # Call appropriate reader
+    if(fileExtension == "mztab") {
+      print("Using readMzTabM()")
+      readMzTabM(filePeakMatrixPath)
+    } else {
+      print("Using readMSDial()")
+      readMSDial(filePeakMatrixPath)
+    }
   } else {
     NULL
   }

R/R_packages.R

@@ -26,7 +26,6 @@ load_metfamily_dependencies <- function() {
   library("FactoMineR")
   library("mixOmics")
   library("pcaMethods")
-  library(searchable)
   library(gdata)
   ##############################################################################################################
   ## tools

R/readMSDial.R

@@ -18,8 +18,8 @@
 #'
 #' @examples
 #' \dontrun{
-#' # Assuming you have an MS-DIAL output file named
-#'  "Metabolite_profile_showcase.txt" in a "data" directory:
+#' # Assuming you have an MS-DIAL output file named 
+#' # "Metabolite_profile_showcase.txt" in a "data" directory:
 #' qf <- readMSDial("data/Metabolite_profile_showcase.txt")
 #'
 #' # Examine the structure of the resulting QFeatures object