From c862f7c1689cecc84702c09a30dfde58bb08ff4b Mon Sep 17 00:00:00 2001
From: Philippine Louail <philippine.louail@outlook.com>
Date: Thu, 1 Feb 2024 15:45:48 +0100
Subject: [PATCH 1/9] MztabParam

---
 DESCRIPTION                      |   3 +-
 NAMESPACE                        |   1 +
 R/AllGenerics.R                  |  14 +-
 R/MzTabParam.R                   | 406 +++++++++++++++++++++++++++++++
 inst/NEWS                        |   8 +-
 man/MzTabParam.Rd                |  99 ++++++++
 man/PlainTextParam.Rd            |   3 +-
 man/RDataParam.Rd                |   3 +-
 man/storeResults.Rd              |  14 +-
 tests/testthat/test_MzTabParam.R |  95 ++++++++
 10 files changed, 638 insertions(+), 8 deletions(-)
 create mode 100644 R/MzTabParam.R
 create mode 100644 man/MzTabParam.Rd
 create mode 100644 tests/testthat/test_MzTabParam.R

diff --git a/DESCRIPTION b/DESCRIPTION
index 005b55868..60a014ecf 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,5 +1,5 @@
 Package: xcms
-Version: 4.1.7
+Version: 4.1.8
 Title: LC-MS and GC-MS Data Analysis
 Description: Framework for processing and visualization of chromatographically
     separated and single-spectra mass spectral data. Imports from AIA/ANDI NetCDF,
@@ -97,6 +97,7 @@ Collate:
     'MPI.R'
     'MsExperiment-functions.R'
     'MsExperiment.R'
+    'MzTabParam.R'
     'PlainTextParam.R'
     'RDataParam.R'
     'XcmsExperiment-functions.R'
diff --git a/NAMESPACE b/NAMESPACE
index aa3563bf3..e0d862fcd 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -596,6 +596,7 @@ importFrom("jsonlite", "serializeJSON", "write_json", "unserializeJSON",
            "read_json")
 export("RDataParam")
 export("PlainTextParam")
+export("MzTabParam")
 exportMethods("storeResults")
 
 ## filtering features things
diff --git a/R/AllGenerics.R b/R/AllGenerics.R
index b9cd7618f..465064e8d 100644
--- a/R/AllGenerics.R
+++ b/R/AllGenerics.R
@@ -2024,7 +2024,8 @@ setGeneric("stitch.netCDF.new", function(object, lockMass) standardGeneric("stit
 #' - [`PlainTextParam`]: Store `MsExperiment` and `XcmsExperiment` objects as a
 #' folder of plain text files, folder path defined in the `path` argument.
 #'
-#' - `MzTabMParam`: Save in MzTab format (to be defined).
+#' - [`MzTabMParam`]: Save an `XcmsExperiment` object as a .mztabm format. file
+#' path defined in the `path` argument.
 #'
 #' For specific examples, see the help pages of the individual parameter classes
 #' listed above.
@@ -2034,7 +2035,7 @@ setGeneric("stitch.netCDF.new", function(object, lockMass) standardGeneric("stit
 #'
 #' @param param The parameter object selecting and configuring the format for
 #' saving. It can be one of the following classes: [`RDataParam`],
-#' [`PlainTextParam`], or `MzTabMParam`.
+#' [`PlainTextParam`], or [`MzTabMParam`].
 #'
 #' @param ... Optional parameters.
 #'
@@ -2059,6 +2060,15 @@ setGeneric("stitch.netCDF.new", function(object, lockMass) standardGeneric("stit
 #' ## Save as a collection of plain text files
 #' storeResults(object = faahko_sub, param = param)
 #'
+#' ## Define param
+#' param <- MzTabParam(studyId = "test",
+#'                     polarity = "positive",
+#'                     sampleDataColumn = "sample_type"
+#'                     path = "test/path/")
+#'
+#' ## Save as a .mzTabm file
+#' storeResults(object = faahko_sub, param = param)
+#'
 #' @md
 setGeneric("storeResults", function(object, param, ...) standardGeneric("storeResults"))
 setGeneric("subset<-", function(object, value) standardGeneric("subset<-"))
diff --git a/R/MzTabParam.R b/R/MzTabParam.R
new file mode 100644
index 000000000..756ae2d8a
--- /dev/null
+++ b/R/MzTabParam.R
@@ -0,0 +1,406 @@
+#' @title Store contents of an `XcmsExperiment` objects as a .mztabm file
+#'
+#' @name MzTabParam
+#'
+#' @export
+#'
+#' @family xcms result export formats.
+#'
+#' @description
+#' The `MzTabParam` class and method enable users to save an `XcmsExperiment`
+#' object as a mzTabm format. Mainly the metadata (MTD) and Small molecule
+#' feature (SMF) tables will represent the `XcmsExperiment`. The small molecule
+#' summary section (SML) will be filled with `null` values as no annotation and
+#' identification of compound is performed in `xcms`.
+#'
+#' This `param` class and method are part of the possible dispatch of the
+#' generic function `storeResults`. The file will be created by calling
+#' `storeResults`. If the file already exists, it will get overwritten.
+#'
+#' @param studyId `character` Will be both the `filename` of the object saved in
+#' .mztabm format and the `mzTab-ID` in the file.
+#'
+#' @param polarity `character` Describes the polarity of the experiment. Two
+#' inputs are possible, "positive" (default) or "negative".
+#'
+#' @param sampleDataColumn `character` strings corresponding to the column name(s)
+#' of the `sampleData()` of the `XcmsExperiment` object with the different
+#' *variables* of the experiment, for example it could be *"phenotype"*,
+#' *"sample_type"*, etc...
+#'
+#' @param path `character(1)` Define where the file is going to be stored. The
+#' default will be `tempdir()`.
+#'
+#' @param optionalFeatureColumns Optional columns from `featureDefinitions`
+#' that should be exported too. For example it could be *"peakidx*,
+#' *"npeaks"*, etc...
+#'
+#' @param dots `list` Correspond to any optional parameters to be passed
+#' to the `featureValues` function. (e.g. parameters `method` or `value`).
+#'
+#' @inheritParams storeResults
+#'
+#' @return for `MzTabParam`: a `MzTabParam` class. `storeResults` does
+#' not return anything but saves the object as a .mztabm file.
+#'
+#' @note
+#' This function was build so that the output fit the recommendation of mztab-m
+#' file format. These can be found here:
+#' http://hupo-psi.github.io/mzTab/2_0-metabolomics-release/mzTab_format_specification_2_0-M_release.html
+#'
+#' @references
+#'
+#' Hoffmann N, Rein J, Sachsenberg T, Hartler J, Haug K, Mayer G, Alka O,
+#' Dayalan S, Pearce JTM, Rocca-Serra P, Qi D, Eisenacher M, Perez-Riverol Y,
+#' Vizcaíno JA, Salek RM, Neumann S, Jones AR. mzTab-M: A Data Standard for
+#' Sharing Quantitative Results in Mass Spectrometry Metabolomics. Anal Chem.
+#' 2019 Mar 5;91(5):3302-3310. doi: 10.1021/acs.analchem.8b04310. Epub 2019 Feb
+#' 13. PMID: 30688441; PMCID: PMC6660005.
+#'
+#' @author Philippine Louail, Johannes Rainer
+#'
+#' @examples
+#' ## Load a test data set with detected peaks, of class `XcmsExperiment`
+#' test_xcms <- loadXcmsData()
+#'
+#' ## Define param
+#' param <- MzTabParam(studyId = "test",
+#'                     polarity = "positive",
+#'                     sampleDataColumn = "sample_type")
+#'
+#' ## Save as a .mzTabm file
+#' storeResults(test_xcms, param)
+#'
+NULL
+
+#' @noRd
+setClass("MzTabParam",
+         slots = c(studyId = "character",
+                   polarity = "character",
+                   sampleDataColumn = "character",
+                   path = "character",
+                   optionalFeatureColumns = "character",
+                   dots = "list"
+                   ),
+         contains = "Param",
+         prototype = prototype(
+             studyId = character(),
+             polarity =  character(),
+             sampleDataColumn = character(),
+             path = character(),
+             optionalFeatureColumns = character(),
+             dots = list()
+         ),
+         validity = function(object) {
+             msg <- NULL
+             if(length(object@studyId) != 1)
+                msg <- c("'studyId' has to be a character string of length 1")
+             if(length(object@polarity) != 1)
+                 msg <- c(msg, "'polarity' has to be a character string of length 1")
+             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
+#'
+#' @export
+MzTabParam <- function(studyId = character(),
+                       polarity = c("positive", "negative"),
+                       sampleDataColumn = character(),
+                       path = tempdir(),
+                       optionalFeatureColumns = character(), ...) {
+    polarity <- match.arg(polarity)
+    new("MzTabParam", studyId = studyId, polarity = polarity,
+        sampleDataColumn = sampleDataColumn, path = path,
+        optionalFeatureColumns = optionalFeatureColumns, dots = list(...))
+}
+
+#' @rdname MzTabParam
+setMethod("storeResults",
+          signature(object = "XcmsExperiment",
+                    param = "MzTabParam"),
+          function(object, param){
+              if(!param@sampleDataColumn %in% colnames(sampleData(object)))
+                  stop("'sampleDataColumn' has to correspond to column names",
+                  "of the sampleData() table")
+              if(length(param@optionalFeatureColumns) != 0)
+                  if(!param@optionalFeatureColumns %in% colnames(featureDefinitions(object)))
+                      stop("'optionalFeatureColumns' have to correspond to",
+                      "column names of the featureDefinitions() table")
+
+              var_list <- unique(.mztab_study_variables(sampleData(object),
+                                                        param@sampleDataColumn))
+              fl <- file.path(param@path, paste0(param@studyId, ".mztab"))
+              if (file.exists(fl)) {
+                  warning("File ", basename(fl), " already exists. ",
+                          "Will overwrite.")
+                  file.remove(fl)
+              }
+              con <- file(fl, open = "at")
+              on.exit(close(con))
+
+              mtd <- .mztab_metadata(object, study_id = param@studyId,
+                                     polarity = param@polarity,
+                                     col_phenotype = param@sampleDataColumn)
+              .mztab_export(mtd, con)
+              writeLines("", con)
+
+              sml <- .mztab_small_molecule_summary(n_sample = length(object),
+                                                   var_list = var_list)
+              .mztab_export(sml, con)
+              writeLines("", con)
+
+              smf <- do.call(.mztab_small_molecule_feature,
+                             c(list(object = object,
+                                    opt_columns = param@optionalFeatureColumns),
+                                    param@dots))
+              .mztab_export(smf, con)
+          })
+
+
+### Helper functions
+
+#' @description
+#'
+#' Create the metadata `matrix` (MTD). Use the .MTD static object as a basis.
+#'
+#' @noRd
+.mztab_metadata <- function(object, study_id, polarity, col_phenotype) {
+    n_sample <- length(object)
+    seq_sample <- seq_len(n_sample)
+    base <- .MTD
+    base[base == "replace_id"]  <- study_id
+    msrun <- cbind(
+        name = paste0("ms_run[", seq_sample, "]-location"),
+        value = unlist(fileNames(object)),
+        order = .prefix_zero(seq_sample)
+    )
+    if (polarity == "positive") {
+        pol <- cbind(
+            name = paste0("ms_run[", seq_sample, "]-scan_polarity[1]"),
+            value = "[MS, MS:1000130, positive scan, ]",
+            order = .prefix_zero(seq_sample))
+    } else {
+        pol <- cbind(
+            name = paste0("ms_run[", seq_sample, "]-scan_polarity[1]"),
+            value = "[MS, MS:1000129, negative scan, ]",
+            order = .prefix_zero(seq_sample))
+    }
+    msrun <- rbind(msrun, pol)
+    msrun <- msrun[order(msrun[, "order"]), c("name", "value")]
+
+    assay <- cbind(
+        name = paste("assay", seq_sample),
+        value = paste0("assay[", seq_sample, "]"),
+        order = .prefix_zero(seq_sample)
+    )
+    assay_ref <- cbind(
+        name = paste0("assay[", seq_sample, "]-ms_run_ref"),
+        value = paste0("ms_run[", seq_sample, "]"),
+        order = .prefix_zero(seq_sample)
+    )
+    assay <- rbind(assay, assay_ref)
+    assay <- assay[order(assay[, "order"]), c("name", "value")]
+
+    var <- .mztab_study_variable_entries(sampleData(object), col_phenotype)
+
+    mtd <- rbind(
+        base[1:4, ],
+        msrun,
+        assay,
+        var,
+        base[5:nrow(base), ]
+    )
+    cbind(id = "MTD", mtd)
+}
+
+#' @description
+#'
+#' Create the *empty* small molecule summary (SML) `matrix`.
+#' Use the .SML static object as a basis
+#'
+#' @noRd
+#'
+#' @examples
+#'
+#' .mztab_small_molecule_summary(5, c(1, 2, 3))
+.mztab_small_molecule_summary <- function(n_sample, var_list) {
+    sml <- c(.SML, paste0("abundance_assay[", seq_len(n_sample) ,"]"),
+             paste0("abundance_study_variable[",
+                    seq_len(length(var_list)) ,"]"),
+             paste0("abundance_variation_study_variable[",
+                    seq_len(length(var_list)) ,"]"))
+    rbind(sml, c("SML", "1", rep("null", length(sml) - 2L)))
+}
+
+#' @description
+#'
+#' Create the small molecule feature (SMF) `matrix` One row is one feature
+#' defined in xcms. Use the .SMF static object.
+#' object as a basis.
+#'
+#' @noRd
+#'
+#' @param object `XcmsExperiment`.
+#'
+#' @param opt_columns `character` defining optional columns in
+#'     `featureDefinitions` that should be exported too.
+#'
+#' @param ... optional parameters for the `featureValues` call.
+.mztab_small_molecule_feature <- function(object, opt_columns = character(),
+                                          ...) {
+    fts <- featureDefinitions(object)
+    smf <- matrix(data = "null", ncol = length(.SMF), nrow = nrow(fts),
+                  dimnames = list(character(), .SMF))
+    smf[, "SFH"] <- "SMF"
+    smf[, "SMF_ID"] <- seq_len(nrow(fts))
+    smf[, "exp_mass_to_charge"] <- as.character(fts$mzmed, digits = 18)
+    smf[, "retention_time_in_seconds"] <- as.character(fts$rtmed, digits = 15)
+    smf[, "retention_time_in_seconds_start"] <- as.character(fts$rtmin,
+                                                             digits = 15)
+    smf[, "retention_time_in_seconds_end"] <- as.character(fts$rtmax,
+                                                           digits = 15)
+
+    fvals <- featureValues(object, ...)
+    colnames(fvals) <- paste0("abundance_assay[", seq_len(ncol(fvals)), "]")
+    fvals <- apply(fvals, 2L, as.character, digits = 15)
+    fvals[is.na(fvals)] <- "null"
+
+    smf <- cbind(smf, fvals)
+
+    if (length(opt_columns)) {
+        tmp <- do.call(
+            cbind, lapply(opt_columns,
+                          function(z) {
+                              if (z == "peakidx") {
+                                  vapply(fts[, z], paste0, character(1),
+                                         collapse = "| ")
+                              } else as.character(fts[, z], digits = 15)
+                          }))
+        colnames(tmp) <- paste0("opt_", opt_columns)
+        smf <- cbind(smf, tmp)
+    }
+    smf <- rbind(colnames(smf), smf)
+    unname(smf)
+}
+
+#' @description
+#'
+#' Define the `character` vector with all study variables.
+#'
+#' @param x `data.frame` with sample annotations
+#'
+#' @param variable `character` with the column name(s) containing the study
+#'     variables.
+#'
+#' @return `character` with the study variables, being a concatenation of
+#'     the column name `"|"` and the value of the variable.
+#'
+#' @noRd
+#'
+#' @examples
+#'
+#' x <- data.frame(sex = c("male", "female", "female", "male", "male"),
+#'                 group = c("case", "case", "control", "case", "control"))
+#'
+#' .mztab_study_variables(x, variable = c("sex", "group"))
+#'
+#' .mztab_study_variables(x, "sex")
+.mztab_study_variables <- function(x = data.frame(), variable = character(),
+                                   sep = ":") {
+    do.call(cbind, lapply(variable, function(z) paste0(z, sep, x[, z])))
+}
+
+#' @description
+#'
+#' Create a `matrix` with the *study_variable* metadata content based.
+#'
+#' @param x `data.frame` representing the `sampleData` of the `MsExperiment`.
+#'
+#' @param variable `character` defining the columns in `x` containing the
+#'     sample variables.
+#'
+#' @return `character` `matrix` (two columns) with the result.
+#'
+#' @noRd
+#'
+#' @examples
+#'
+#' .mztab_study_variable_entries(x, "sex")
+#'
+#' .mztab_study_variable_entries(x, c("group", "sex"))
+.mztab_study_variable_entries <- function(x, variable, sep = "| ") {
+    svar <- .mztab_study_variables(x, variable)
+    unique_svar <- unique(as.vector(svar))
+    res <- matrix(character(), ncol = 2, nrow = 0,
+                  dimnames = list(character(), c("name", "value")))
+    for (i in seq_along(unique_svar)) {
+        idx <- which(svar == unique_svar[i], arr.ind = TRUE)
+        res <- rbind(
+            res,
+            matrix(ncol = 2,
+            c(paste0("study_variable[", i, "]"),
+              paste0("study_variable[", i, "]-assay_refs"),
+              paste0(unique_svar[i]),
+              paste0("assay[", idx[, "row"], "]", collapse = sep)
+              )))
+    }
+    res
+}
+
+#' @noRd
+.prefix_zero <- function(x) {
+    sprintf(paste0("%0", ceiling(log10(max(x) + 1)), "d"), x)
+}
+
+#' @noRd
+.mztab_export <- function(x, con) {
+    x <- apply(x, 1L, paste0, collapse = "\t")
+    writeLines(x, con)
+}
+
+### Static objects
+.MTD <- cbind(
+    name = c("mzTab-version",
+             "mzTab-ID",
+             "software[1]",
+             "quantification_method",
+             "cv[1]-label",
+             "cv[1]-full_name",
+             "cv[1]-version",
+             "cv[1]-uri",
+             "database[1]",
+             "database[1]-prefix",
+             "database[1]-version",
+             "database[1]-uri",
+             "small_molecule-quantification_unit",
+             "small_molecule_feature-quantification_unit",
+             "id_confidence_measure[1]"),
+    value = c("2.0.0-M",
+              "replace_id",
+              "[MS, MS:4711, xcms, 3.1.1]",
+              "[MS, MS:1001834, LC-MS label-free quantitation analysis]",
+              "MS",
+              "PSI-MS controlled vocabulary",
+              "4.1.138",
+              "https://raw.githubusercontent.com/HUPO-PSI/psi-ms-CV/master/psi-ms.obo",
+              "[,, \"no database\", null ]",
+              "null",
+              "Unknown",
+              "null",
+              "null",
+              "[MS, MS:1001841, LC-MS feature volume, ]",
+              "null"))
+
+.SML <- c("SMH", "SML_ID","SMF_ID_REFS", "database_identifier",
+          "chemical_formula", "smiles", "inchi", "chemical_name",
+          "uri", "theoretical_neutral_mass", "adduct_ions", "reliability",
+          "best_id_confidence_measure", "best_id_confidence_value")
+
+.SMF <- c("SFH", "SMF_ID","SME_ID_REFS", "SME_ID_REF_ambiguity_code",
+          "adduct_ion", "isotopomer", "exp_mass_to_charge", "charge",
+          "retention_time_in_seconds", "retention_time_in_seconds_start",
+          "retention_time_in_seconds_end")
diff --git a/inst/NEWS b/inst/NEWS
index 5fc15922b..6d84b4881 100644
--- a/inst/NEWS
+++ b/inst/NEWS
@@ -1,3 +1,9 @@
+Changes in version 4.1.8
+----------------------
+
+- Add a `param =` to generic function `storeResults`: `MzTabParam` to save
+  an `XcmsExperiment` object as .mztabm file type.
+
 Changes in version 4.1.7
 ----------------------
 
@@ -56,7 +62,7 @@ Changes in version 4.1.2
 ----------------------
 
 - Add a `param =` to generic function `storeResults`: `PlainTextParam` to save
-  an `XcmsExperiment` or `MsExperiment` object as colleciton of plain text
+  an `XcmsExperiment` or `MsExperiment` object as collection of plain text
   files.
 
 Changes in version 4.1.1
diff --git a/man/MzTabParam.Rd b/man/MzTabParam.Rd
new file mode 100644
index 000000000..f142657c5
--- /dev/null
+++ b/man/MzTabParam.Rd
@@ -0,0 +1,99 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/MzTabParam.R
+\name{MzTabParam}
+\alias{MzTabParam}
+\alias{storeResults,XcmsExperiment,MzTabParam-method}
+\title{Store contents of an `XcmsExperiment` objects as a .mztabm file}
+\usage{
+MzTabParam(
+  studyId = character(),
+  polarity = c("positive", "negative"),
+  sampleDataColumn = character(),
+  path = tempdir(),
+  optionalFeatureColumns = character(),
+  ...
+)
+
+\S4method{storeResults}{XcmsExperiment,MzTabParam}(object, param)
+}
+\arguments{
+\item{studyId}{`character` Will be both the `filename` of the object saved in
+.mztabm format and the `mzTab-ID` in the file.}
+
+\item{polarity}{`character` Describes the polarity of the experiment. Two
+inputs are possible, "positive" (default) or "negative".}
+
+\item{sampleDataColumn}{`character` strings corresponding to the column name(s)
+of the `sampleData()` of the `XcmsExperiment` object with the different
+*variables* of the experiment, for example it could be *"phenotype"*,
+*"sample_type"*, etc...}
+
+\item{path}{`character(1)` Define where the file is going to be stored. The
+default will be `tempdir()`.}
+
+\item{optionalFeatureColumns}{Optional columns from `featureDefinitions`
+that should be exported too. For example it could be *"peakidx*,
+*"npeaks"*, etc...}
+
+\item{...}{Optional parameters.}
+
+\item{object}{\code{MsExperiment} or \code{XcmsExperiment} The data object that needs
+to be saved.}
+
+\item{param}{The parameter object selecting and configuring the format for
+saving. It can be one of the following classes: \code{\link{RDataParam}},
+\code{\link{PlainTextParam}}, or \code{\link{MzTabMParam}}.}
+
+\item{dots}{`list` Correspond to any optional parameters to be passed
+to the `featureValues` function. (e.g. parameters `method` or `value`).}
+}
+\value{
+for `MzTabParam`: a `MzTabParam` class. `storeResults` does
+not return anything but saves the object as a .mztabm file.
+}
+\description{
+The `MzTabParam` class and method enable users to save an `XcmsExperiment`
+object as a mzTabm format. Mainly the metadata (MTD) and Small molecule
+feature (SMF) tables will represent the `XcmsExperiment`. The small molecule
+summary section (SML) will be filled with `null` values as no annotation and
+identification of compound is performed in `xcms`.
+
+This `param` class and method are part of the possible dispatch of the
+generic function `storeResults`. The file will be created by calling
+`storeResults`. If the file already exists, it will get overwritten.
+}
+\note{
+This function was build so that the output fit the recommendation of mztab-m
+file format. These can be found here:
+http://hupo-psi.github.io/mzTab/2_0-metabolomics-release/mzTab_format_specification_2_0-M_release.html
+}
+\examples{
+## Load a test data set with detected peaks, of class `XcmsExperiment`
+test_xcms <- loadXcmsData()
+
+## Define param
+param <- MzTabParam(studyId = "test",
+                    polarity = "positive",
+                    sampleDataColumn = "sample_type")
+
+## Save as a .mzTabm file
+storeResults(test_xcms, param)
+
+}
+\references{
+Hoffmann N, Rein J, Sachsenberg T, Hartler J, Haug K, Mayer G, Alka O,
+Dayalan S, Pearce JTM, Rocca-Serra P, Qi D, Eisenacher M, Perez-Riverol Y,
+Vizcaíno JA, Salek RM, Neumann S, Jones AR. mzTab-M: A Data Standard for
+Sharing Quantitative Results in Mass Spectrometry Metabolomics. Anal Chem.
+2019 Mar 5;91(5):3302-3310. doi: 10.1021/acs.analchem.8b04310. Epub 2019 Feb
+13. PMID: 30688441; PMCID: PMC6660005.
+}
+\seealso{
+Other xcms result export formats.: 
+\code{\link{PlainTextParam}},
+\code{\link{RDataParam}}
+}
+\author{
+Philippine Louail, Johannes Rainer
+}
+\concept{xcms result export formats.}
diff --git a/man/PlainTextParam.Rd b/man/PlainTextParam.Rd
index 8bd806486..46f094294 100644
--- a/man/PlainTextParam.Rd
+++ b/man/PlainTextParam.Rd
@@ -22,7 +22,7 @@ to be saved.}
 
 \item{param}{The parameter object selecting and configuring the format for
 saving. It can be one of the following classes: \code{\link{RDataParam}},
-\code{\link{PlainTextParam}}, or \code{MzTabMParam}.}
+\code{\link{PlainTextParam}}, or \code{\link{MzTabMParam}}.}
 }
 \value{
 for `PlainTextParam`: a `PlainTextParam` class. `storeResults` does
@@ -106,6 +106,7 @@ storeResults(object = faahko_sub, param = param)
 }
 \seealso{
 Other xcms result export formats.: 
+\code{\link{MzTabParam}},
 \code{\link{RDataParam}}
 }
 \author{
diff --git a/man/RDataParam.Rd b/man/RDataParam.Rd
index 617c3dc93..7da2d9dd1 100644
--- a/man/RDataParam.Rd
+++ b/man/RDataParam.Rd
@@ -18,7 +18,7 @@ to be saved.}
 
 \item{param}{The parameter object selecting and configuring the format for
 saving. It can be one of the following classes: \code{\link{RDataParam}},
-\code{\link{PlainTextParam}}, or \code{MzTabMParam}.}
+\code{\link{PlainTextParam}}, or \code{\link{MzTabMParam}}.}
 }
 \value{
 for `RDataParam`: a `RDataParam` class. `storeResults` does not
@@ -44,6 +44,7 @@ storeResults(object = faahko_sub, param = param)
 }
 \seealso{
 Other xcms result export formats.: 
+\code{\link{MzTabParam}},
 \code{\link{PlainTextParam}}
 }
 \author{
diff --git a/man/storeResults.Rd b/man/storeResults.Rd
index a72a4c8cd..d435e30c3 100644
--- a/man/storeResults.Rd
+++ b/man/storeResults.Rd
@@ -12,7 +12,7 @@ to be saved.}
 
 \item{param}{The parameter object selecting and configuring the format for
 saving. It can be one of the following classes: \code{\link{RDataParam}},
-\code{\link{PlainTextParam}}, or \code{MzTabMParam}.}
+\code{\link{PlainTextParam}}, or \code{\link{MzTabMParam}}.}
 
 \item{...}{Optional parameters.}
 }
@@ -27,7 +27,8 @@ Supported \code{param} objects are:
 specified in the \code{fileName} argument.
 \item \code{\link{PlainTextParam}}: Store \code{MsExperiment} and \code{XcmsExperiment} objects as a
 folder of plain text files, folder path defined in the \code{path} argument.
-\item \code{MzTabMParam}: Save in MzTab format (to be defined).
+\item \code{\link{MzTabMParam}}: Save an \code{XcmsExperiment} object as a .mztabm format. file
+path defined in the \code{path} argument.
 }
 
 For specific examples, see the help pages of the individual parameter classes
@@ -50,6 +51,15 @@ param <- PlainTextParam(path = "test/path/")
 ## Save as a collection of plain text files
 storeResults(object = faahko_sub, param = param)
 
+## Define param
+param <- MzTabParam(studyId = "test",
+                    polarity = "positive",
+                    sampleDataColumn = "sample_type"
+                    path = "test/path/")
+
+## Save as a .mzTabm file
+storeResults(object = faahko_sub, param = param)
+
 }
 \author{
 Philippine Louail
diff --git a/tests/testthat/test_MzTabParam.R b/tests/testthat/test_MzTabParam.R
new file mode 100644
index 000000000..372f34dc8
--- /dev/null
+++ b/tests/testthat/test_MzTabParam.R
@@ -0,0 +1,95 @@
+faahko <- loadXcmsData("faahko_sub2")
+faahko <- groupChromPeaks(
+    faahko, PeakDensityParam(sampleGroups = rep(1, length(faahko))))
+
+xmse_full <- loadXcmsData()
+
+test_that(".mztab_metadata works", {
+    mtd <- .mztab_metadata(xmse_full, study_id = "test", polarity = "negative",
+                         col_phenotype = "sample_type")
+
+    expect_false(all(mtd != "test"))
+    expect_true(is.matrix(mtd))
+    expect_true(is.character(mtd))
+    expect_equal(mtd[, "id"], rep("MTD", nrow(mtd)))
+    expect_equal(ncol(mtd), 3)
+    expect_equal(length(grep("assay ", mtd[, 2])), length(xmse_full))
+    expect_equal(length(grep("negative ", mtd[, 3])), length(xmse_full))
+})
+
+test_that(".mztab_small_molecule_feature works", {
+    a <- .mztab_small_molecule_feature(faahko)
+    expect_true(is.matrix(a))
+    expect_true(is.character(a))
+    expect_equal(a[1, 1], "SFH")
+    expect_equal(nrow(a), nrow(featureDefinitions(faahko)) + 1)
+    expect_equal(length(grep("abundance_assay", a[1, ])), length(faahko))
+
+    b <- .mztab_small_molecule_feature(
+        faahko, opt_columns = c("peakidx", "ms_level"),
+        method = "sum", value = "maxo")
+    expect_equal(nrow(a), nrow(b))
+    expect_true(ncol(b) > ncol(a))
+    expect_true(any(b[1, ] == "opt_peakidx"))
+    expect_true(any(b[1, ] == "opt_ms_level"))
+    ## Check that optional parameters are correctly passed
+    a2 <- a[2:nrow(a), a[1, ] == "abundance_assay[2]"]
+    a2[a2 == "null"] <- NA
+    a2 <- as.numeric(a2)
+    b2 <- b[2:nrow(b), b[1, ] == "abundance_assay[2]"]
+    b2[b2 == "null"] <- NA
+    b2 <- as.numeric(b2)
+    expect_equal(is.na(a2), is.na(b2))
+    expect_true(all(a2[!is.na(a2)] != b2[!is.na(b2)]))
+    ## Check that we don't loose information through import/export
+    expect_equal(a2, unname(featureValues(faahko)[, 2]))
+    expect_equal(b2, unname(featureValues(
+        faahko, method = "sum", value = "maxo")[, 2]))
+})
+
+test_that(".mztab_study_variables works", {
+    x <- data.frame(a = 1:3, b = c(1, 1, 2))
+    res <- .mztab_study_variables(x, variable = "a")
+    expect_true(is.character(res))
+    expect_true(is.matrix(res))
+    expect_true(ncol(res) == 1L)
+    expect_equal(res[, 1L], c("a:1", "a:2", "a:3"))
+
+    res <- .mztab_study_variables(x, variable = c("a", "b"))
+    expect_true(is.character(res))
+    expect_true(is.matrix(res))
+    expect_true(ncol(res) == 2L)
+    expect_equal(res[, 1L], c("a:1", "a:2", "a:3"))
+    expect_equal(res[, 2L], c("b:1", "b:1", "b:2"))
+})
+
+test_that(".mztab_study_variable_entries works", {
+    x <- data.frame(a = 1:3, b = c(1, 1, 2))
+    res <- .mztab_study_variable_entries(x, variable = "a")
+    expect_true(is.character(res))
+    expect_true(is.matrix(res))
+    expect_true(ncol(res) == 2L)
+    expect_equal(unname(res[1, 1]), "study_variable[1]")
+    expect_equal(unname(res[2, 1]), "study_variable[1]-assay_refs")
+    expect_equal(unname(res[1, 2]), "a:1")
+    expect_equal(unname(res[2, 2]), "assay[1]")
+
+    res2 <- .mztab_study_variable_entries(x, variable = c("a", "b"))
+    expect_true(length(res2) > length(res))
+})
+
+test_that("storeResults,MzTabParam works", {
+    d <- tempdir()
+    p <- MzTabParam(studyId = "test_study", path = d,
+                    sampleDataColumn = "sample_index",
+                    optionalFeatureColumns = "peakidx")
+    storeResults(faahko, p)
+    expect_true(file.exists(file.path(d, "test_study.mztab")))
+    res <- readLines(file.path(d, "test_study.mztab"))
+    expect_true(length(res) > 0L)
+    expect_true(length(grep("^MTD", res)) > 0)
+    expect_true(length(grep("^SML", res)) > 0)
+    expect_true(length(grep("^SMF", res)) > 0)
+    ## Check for empty lines
+    expect_true(length(grep(c("^MTD|SML|SMF"), res, invert = TRUE)) == 2)
+})

From 8dd469bd433b554fb6159c0e547f16a12871e7c9 Mon Sep 17 00:00:00 2001
From: Philippine Louail <philippine.louail@outlook.com>
Date: Fri, 2 Feb 2024 09:50:14 +0100
Subject: [PATCH 2/9] fixes

---
 R/AllGenerics.R       | 11 +++++++----
 R/MzTabParam.R        |  6 +++---
 man/MzTabParam.Rd     | 16 ++++++++++------
 man/PlainTextParam.Rd |  2 +-
 man/RDataParam.Rd     |  2 +-
 man/storeResults.Rd   | 11 +++++++----
 6 files changed, 29 insertions(+), 19 deletions(-)

diff --git a/R/AllGenerics.R b/R/AllGenerics.R
index 465064e8d..3cea0d758 100644
--- a/R/AllGenerics.R
+++ b/R/AllGenerics.R
@@ -2024,7 +2024,7 @@ setGeneric("stitch.netCDF.new", function(object, lockMass) standardGeneric("stit
 #' - [`PlainTextParam`]: Store `MsExperiment` and `XcmsExperiment` objects as a
 #' folder of plain text files, folder path defined in the `path` argument.
 #'
-#' - [`MzTabMParam`]: Save an `XcmsExperiment` object as a .mztabm format. file
+#' - [`MzTabParam`]: Save an `XcmsExperiment` object as a .mztabm format. file
 #' path defined in the `path` argument.
 #'
 #' For specific examples, see the help pages of the individual parameter classes
@@ -2035,7 +2035,7 @@ setGeneric("stitch.netCDF.new", function(object, lockMass) standardGeneric("stit
 #'
 #' @param param The parameter object selecting and configuring the format for
 #' saving. It can be one of the following classes: [`RDataParam`],
-#' [`PlainTextParam`], or [`MzTabMParam`].
+#' [`PlainTextParam`], or [`MzTabParam`].
 #'
 #' @param ... Optional parameters.
 #'
@@ -2060,14 +2060,17 @@ setGeneric("stitch.netCDF.new", function(object, lockMass) standardGeneric("stit
 #' ## Save as a collection of plain text files
 #' storeResults(object = faahko_sub, param = param)
 #'
+#' ## Get XcmsExperiment object with defined metadata
+#' test_xcms <- loadXcmsData()
+#'
 #' ## Define param
 #' param <- MzTabParam(studyId = "test",
 #'                     polarity = "positive",
-#'                     sampleDataColumn = "sample_type"
+#'                     sampleDataColumn = "sample_type",
 #'                     path = "test/path/")
 #'
 #' ## Save as a .mzTabm file
-#' storeResults(object = faahko_sub, param = param)
+#' storeResults(object = test_xcms, param = param)
 #'
 #' @md
 setGeneric("storeResults", function(object, param, ...) standardGeneric("storeResults"))
diff --git a/R/MzTabParam.R b/R/MzTabParam.R
index 756ae2d8a..8563e4407 100644
--- a/R/MzTabParam.R
+++ b/R/MzTabParam.R
@@ -35,7 +35,7 @@
 #' that should be exported too. For example it could be *"peakidx*,
 #' *"npeaks"*, etc...
 #'
-#' @param dots `list` Correspond to any optional parameters to be passed
+#' @slot dots `list` Correspond to any optional parameters to be passed
 #' to the `featureValues` function. (e.g. parameters `method` or `value`).
 #'
 #' @inheritParams storeResults
@@ -46,13 +46,13 @@
 #' @note
 #' This function was build so that the output fit the recommendation of mztab-m
 #' file format. These can be found here:
-#' http://hupo-psi.github.io/mzTab/2_0-metabolomics-release/mzTab_format_specification_2_0-M_release.html
+#' (http://hupo-psi.github.io/mzTab/2_0-metabolomics-release/mzTab_format_specification_2_0-M_release.html)
 #'
 #' @references
 #'
 #' Hoffmann N, Rein J, Sachsenberg T, Hartler J, Haug K, Mayer G, Alka O,
 #' Dayalan S, Pearce JTM, Rocca-Serra P, Qi D, Eisenacher M, Perez-Riverol Y,
-#' Vizcaíno JA, Salek RM, Neumann S, Jones AR. mzTab-M: A Data Standard for
+#' Vizcaino JA, Salek RM, Neumann S, Jones AR. mzTab-M: A Data Standard for
 #' Sharing Quantitative Results in Mass Spectrometry Metabolomics. Anal Chem.
 #' 2019 Mar 5;91(5):3302-3310. doi: 10.1021/acs.analchem.8b04310. Epub 2019 Feb
 #' 13. PMID: 30688441; PMCID: PMC6660005.
diff --git a/man/MzTabParam.Rd b/man/MzTabParam.Rd
index f142657c5..9c0591332 100644
--- a/man/MzTabParam.Rd
+++ b/man/MzTabParam.Rd
@@ -42,10 +42,7 @@ to be saved.}
 
 \item{param}{The parameter object selecting and configuring the format for
 saving. It can be one of the following classes: \code{\link{RDataParam}},
-\code{\link{PlainTextParam}}, or \code{\link{MzTabMParam}}.}
-
-\item{dots}{`list` Correspond to any optional parameters to be passed
-to the `featureValues` function. (e.g. parameters `method` or `value`).}
+\code{\link{PlainTextParam}}, or \code{\link{MzTabParam}}.}
 }
 \value{
 for `MzTabParam`: a `MzTabParam` class. `storeResults` does
@@ -62,10 +59,17 @@ This `param` class and method are part of the possible dispatch of the
 generic function `storeResults`. The file will be created by calling
 `storeResults`. If the file already exists, it will get overwritten.
 }
+\section{Slots}{
+
+\describe{
+\item{\code{dots}}{`list` Correspond to any optional parameters to be passed
+to the `featureValues` function. (e.g. parameters `method` or `value`).}
+}}
+
 \note{
 This function was build so that the output fit the recommendation of mztab-m
 file format. These can be found here:
-http://hupo-psi.github.io/mzTab/2_0-metabolomics-release/mzTab_format_specification_2_0-M_release.html
+(http://hupo-psi.github.io/mzTab/2_0-metabolomics-release/mzTab_format_specification_2_0-M_release.html)
 }
 \examples{
 ## Load a test data set with detected peaks, of class `XcmsExperiment`
@@ -83,7 +87,7 @@ storeResults(test_xcms, param)
 \references{
 Hoffmann N, Rein J, Sachsenberg T, Hartler J, Haug K, Mayer G, Alka O,
 Dayalan S, Pearce JTM, Rocca-Serra P, Qi D, Eisenacher M, Perez-Riverol Y,
-Vizcaíno JA, Salek RM, Neumann S, Jones AR. mzTab-M: A Data Standard for
+Vizcaino JA, Salek RM, Neumann S, Jones AR. mzTab-M: A Data Standard for
 Sharing Quantitative Results in Mass Spectrometry Metabolomics. Anal Chem.
 2019 Mar 5;91(5):3302-3310. doi: 10.1021/acs.analchem.8b04310. Epub 2019 Feb
 13. PMID: 30688441; PMCID: PMC6660005.
diff --git a/man/PlainTextParam.Rd b/man/PlainTextParam.Rd
index 46f094294..69c50266b 100644
--- a/man/PlainTextParam.Rd
+++ b/man/PlainTextParam.Rd
@@ -22,7 +22,7 @@ to be saved.}
 
 \item{param}{The parameter object selecting and configuring the format for
 saving. It can be one of the following classes: \code{\link{RDataParam}},
-\code{\link{PlainTextParam}}, or \code{\link{MzTabMParam}}.}
+\code{\link{PlainTextParam}}, or \code{\link{MzTabParam}}.}
 }
 \value{
 for `PlainTextParam`: a `PlainTextParam` class. `storeResults` does
diff --git a/man/RDataParam.Rd b/man/RDataParam.Rd
index 7da2d9dd1..ce2536f1e 100644
--- a/man/RDataParam.Rd
+++ b/man/RDataParam.Rd
@@ -18,7 +18,7 @@ to be saved.}
 
 \item{param}{The parameter object selecting and configuring the format for
 saving. It can be one of the following classes: \code{\link{RDataParam}},
-\code{\link{PlainTextParam}}, or \code{\link{MzTabMParam}}.}
+\code{\link{PlainTextParam}}, or \code{\link{MzTabParam}}.}
 }
 \value{
 for `RDataParam`: a `RDataParam` class. `storeResults` does not
diff --git a/man/storeResults.Rd b/man/storeResults.Rd
index d435e30c3..c4da3169d 100644
--- a/man/storeResults.Rd
+++ b/man/storeResults.Rd
@@ -12,7 +12,7 @@ to be saved.}
 
 \item{param}{The parameter object selecting and configuring the format for
 saving. It can be one of the following classes: \code{\link{RDataParam}},
-\code{\link{PlainTextParam}}, or \code{\link{MzTabMParam}}.}
+\code{\link{PlainTextParam}}, or \code{\link{MzTabParam}}.}
 
 \item{...}{Optional parameters.}
 }
@@ -27,7 +27,7 @@ Supported \code{param} objects are:
 specified in the \code{fileName} argument.
 \item \code{\link{PlainTextParam}}: Store \code{MsExperiment} and \code{XcmsExperiment} objects as a
 folder of plain text files, folder path defined in the \code{path} argument.
-\item \code{\link{MzTabMParam}}: Save an \code{XcmsExperiment} object as a .mztabm format. file
+\item \code{\link{MzTabParam}}: Save an \code{XcmsExperiment} object as a .mztabm format. file
 path defined in the \code{path} argument.
 }
 
@@ -51,14 +51,17 @@ param <- PlainTextParam(path = "test/path/")
 ## Save as a collection of plain text files
 storeResults(object = faahko_sub, param = param)
 
+## Get XcmsExperiment object with defined metadata
+test_xcms <- loadXcmsData()
+
 ## Define param
 param <- MzTabParam(studyId = "test",
                     polarity = "positive",
-                    sampleDataColumn = "sample_type"
+                    sampleDataColumn = "sample_type",
                     path = "test/path/")
 
 ## Save as a .mzTabm file
-storeResults(object = faahko_sub, param = param)
+storeResults(object = test_xcms, param = param)
 
 }
 \author{

From a45ff100881c7c781bd1b4d0cdddacab00dab4e2 Mon Sep 17 00:00:00 2001
From: Philippine Louail <philippine.louail@outlook.com>
Date: Thu, 18 Jul 2024 10:43:18 +0200
Subject: [PATCH 3/9] Update MzTabParam.R

---
 R/MzTabParam.R | 36 +++++++++++++++++++++++-------------
 1 file changed, 23 insertions(+), 13 deletions(-)

diff --git a/R/MzTabParam.R b/R/MzTabParam.R
index 8563e4407..0b80eafc0 100644
--- a/R/MzTabParam.R
+++ b/R/MzTabParam.R
@@ -175,7 +175,7 @@ setMethod("storeResults",
     base[base == "replace_id"]  <- study_id
     msrun <- cbind(
         name = paste0("ms_run[", seq_sample, "]-location"),
-        value = unlist(fileNames(object)),
+        value = paste0("file:///", unlist(gsub(" ", "",fileNames(object)))),
         order = .prefix_zero(seq_sample)
     )
     if (polarity == "positive") {
@@ -193,8 +193,8 @@ setMethod("storeResults",
     msrun <- msrun[order(msrun[, "order"]), c("name", "value")]
 
     assay <- cbind(
-        name = paste("assay", seq_sample),
-        value = paste0("assay[", seq_sample, "]"),
+        name = paste0("assay[", seq_sample, "]"),
+        value = paste(seq_sample, "assay"),
         order = .prefix_zero(seq_sample)
     )
     assay_ref <- cbind(
@@ -214,7 +214,9 @@ setMethod("storeResults",
         var,
         base[5:nrow(base), ]
     )
-    cbind(id = "MTD", mtd)
+    mtd <- cbind(id = "MTD", mtd)
+
+    gsub("\\\\", "/", mtd)
 }
 
 #' @description
@@ -241,7 +243,7 @@ setMethod("storeResults",
 #' Create the small molecule feature (SMF) `matrix` One row is one feature
 #' defined in xcms. Use the .SMF static object.
 #' object as a basis.
-#'
+#'read
 #' @noRd
 #'
 #' @param object `XcmsExperiment`.
@@ -343,8 +345,10 @@ setMethod("storeResults",
             res,
             matrix(ncol = 2,
             c(paste0("study_variable[", i, "]"),
+              paste0("study_variable[", i, "]-description"),
               paste0("study_variable[", i, "]-assay_refs"),
               paste0(unique_svar[i]),
+              paste0("Sample in column ", unique_svar[i]), #either this or <to be filled>
               paste0("assay[", idx[, "row"], "]", collapse = sep)
               )))
     }
@@ -363,6 +367,7 @@ setMethod("storeResults",
 }
 
 ### Static objects
+
 .MTD <- cbind(
     name = c("mzTab-version",
              "mzTab-ID",
@@ -372,28 +377,32 @@ setMethod("storeResults",
              "cv[1]-full_name",
              "cv[1]-version",
              "cv[1]-uri",
+             "cv[2]-label",
+             "cv[2]-full_name",
+             "cv[2]-version",
+             "cv[2]-uri",
              "database[1]",
              "database[1]-prefix",
              "database[1]-version",
              "database[1]-uri",
-             "small_molecule-quantification_unit",
-             "small_molecule_feature-quantification_unit",
-             "id_confidence_measure[1]"),
+             "small_molecule_feature-quantification_unit"),
     value = c("2.0.0-M",
               "replace_id",
-              "[MS, MS:4711, xcms, 3.1.1]",
-              "[MS, MS:1001834, LC-MS label-free quantitation analysis]",
+              "[MS, MS:1001582, XCMS, 3.1.1]",
+              "[MS, MS:1001834, LC-MS label-free quantitation analysis, ]",
               "MS",
               "PSI-MS controlled vocabulary",
               "4.1.138",
               "https://raw.githubusercontent.com/HUPO-PSI/psi-ms-CV/master/psi-ms.obo",
+              "PRIDE",
+              "PRIDE PRoteomics IDEntifications (PRIDE) database controlled vocabulary",
+              "16:10:2023 11:38",
+              "https://www.ebi.ac.uk/ols/ontologies/pride",
               "[,, \"no database\", null ]",
               "null",
               "Unknown",
               "null",
-              "null",
-              "[MS, MS:1001841, LC-MS feature volume, ]",
-              "null"))
+              "[PRIDE, PRIDE:0000330, Arbitrary quantification unit, ]"))
 
 .SML <- c("SMH", "SML_ID","SMF_ID_REFS", "database_identifier",
           "chemical_formula", "smiles", "inchi", "chemical_name",
@@ -404,3 +413,4 @@ setMethod("storeResults",
           "adduct_ion", "isotopomer", "exp_mass_to_charge", "charge",
           "retention_time_in_seconds", "retention_time_in_seconds_start",
           "retention_time_in_seconds_end")
+

From c403cd6b29fe141c640034e8c85723d7b8abce19 Mon Sep 17 00:00:00 2001
From: Philippine Louail <127301965+philouail@users.noreply.github.com>
Date: Tue, 1 Oct 2024 21:54:40 +0200
Subject: [PATCH 4/9] small_update to matchLamaChromPeaks() output

---
 R/XcmsExperiment.R                            |  2 +-
 R/do_adjustRtime-functions.R                  |  7 +-
 tests/testthat/test_MzTabParam.R              | 95 -------------------
 .../testthat/test_do_adjustRtime-functions.R  | 11 ++-
 4 files changed, 13 insertions(+), 102 deletions(-)
 delete mode 100644 tests/testthat/test_MzTabParam.R

diff --git a/R/XcmsExperiment.R b/R/XcmsExperiment.R
index db3efa05f..a094a7163 100644
--- a/R/XcmsExperiment.R
+++ b/R/XcmsExperiment.R
@@ -1391,7 +1391,7 @@ setMethod(
         rt_adj <- bpmapply(rtMap, rt_raw, idx, FUN = function(x, y, i, param) {
             if (nrow(x) >= 10) { # too strict ? Gam always throws error when less than that and loess does not work that well either.
                 .adjust_rt_model(y, method = param@method,
-                                 rt_map = x, span = param@span,
+                                 rt_map = x[, c("ref","obs")], span = param@span,
                                  resid_ratio = param@outlierTolerance,
                                  zero_weight = param@zeroWeight,
                                  bs = param@bs)
diff --git a/R/do_adjustRtime-functions.R b/R/do_adjustRtime-functions.R
index c45b0940a..1fe5282cb 100644
--- a/R/do_adjustRtime-functions.R
+++ b/R/do_adjustRtime-functions.R
@@ -788,7 +788,9 @@ NULL
 #'
 #' @return a `data.frame` with columns `"ref"` and `"obs"` with the retention
 #'     times of the pairs of matched peaks. This `data.frame` can be used
-#'     in `.adjust_rt_model`'s parameter `rt_raw`.
+#'     in `.adjust_rt_model`'s parameter `rt_raw`. The column `chromPeaksId`
+#'     contains the rownames of the `obs_peaks` matrix. This can be used to
+#'     identify the peaks that were matched.
 #'
 #' @author Johannes Rainer, Philippine Louail
 #'
@@ -804,7 +806,8 @@ NULL
     dups <- idx[duplicated(idx[, 2L]), 2L]
     idx <- idx[!idx[, 2L] %in% dups, , drop = FALSE]
     data.frame(ref = ref_anchors[idx[, 2L], 2L],
-               obs = obs_peaks[idx[, 1L], 2L])
+               obs = obs_peaks[idx[, 1L], 2L],
+               chromPeaksId = rownames(obs_peaks[idx[, 1L], ,drop = FALSE]))
 }
 
 #' @description
diff --git a/tests/testthat/test_MzTabParam.R b/tests/testthat/test_MzTabParam.R
deleted file mode 100644
index 372f34dc8..000000000
--- a/tests/testthat/test_MzTabParam.R
+++ /dev/null
@@ -1,95 +0,0 @@
-faahko <- loadXcmsData("faahko_sub2")
-faahko <- groupChromPeaks(
-    faahko, PeakDensityParam(sampleGroups = rep(1, length(faahko))))
-
-xmse_full <- loadXcmsData()
-
-test_that(".mztab_metadata works", {
-    mtd <- .mztab_metadata(xmse_full, study_id = "test", polarity = "negative",
-                         col_phenotype = "sample_type")
-
-    expect_false(all(mtd != "test"))
-    expect_true(is.matrix(mtd))
-    expect_true(is.character(mtd))
-    expect_equal(mtd[, "id"], rep("MTD", nrow(mtd)))
-    expect_equal(ncol(mtd), 3)
-    expect_equal(length(grep("assay ", mtd[, 2])), length(xmse_full))
-    expect_equal(length(grep("negative ", mtd[, 3])), length(xmse_full))
-})
-
-test_that(".mztab_small_molecule_feature works", {
-    a <- .mztab_small_molecule_feature(faahko)
-    expect_true(is.matrix(a))
-    expect_true(is.character(a))
-    expect_equal(a[1, 1], "SFH")
-    expect_equal(nrow(a), nrow(featureDefinitions(faahko)) + 1)
-    expect_equal(length(grep("abundance_assay", a[1, ])), length(faahko))
-
-    b <- .mztab_small_molecule_feature(
-        faahko, opt_columns = c("peakidx", "ms_level"),
-        method = "sum", value = "maxo")
-    expect_equal(nrow(a), nrow(b))
-    expect_true(ncol(b) > ncol(a))
-    expect_true(any(b[1, ] == "opt_peakidx"))
-    expect_true(any(b[1, ] == "opt_ms_level"))
-    ## Check that optional parameters are correctly passed
-    a2 <- a[2:nrow(a), a[1, ] == "abundance_assay[2]"]
-    a2[a2 == "null"] <- NA
-    a2 <- as.numeric(a2)
-    b2 <- b[2:nrow(b), b[1, ] == "abundance_assay[2]"]
-    b2[b2 == "null"] <- NA
-    b2 <- as.numeric(b2)
-    expect_equal(is.na(a2), is.na(b2))
-    expect_true(all(a2[!is.na(a2)] != b2[!is.na(b2)]))
-    ## Check that we don't loose information through import/export
-    expect_equal(a2, unname(featureValues(faahko)[, 2]))
-    expect_equal(b2, unname(featureValues(
-        faahko, method = "sum", value = "maxo")[, 2]))
-})
-
-test_that(".mztab_study_variables works", {
-    x <- data.frame(a = 1:3, b = c(1, 1, 2))
-    res <- .mztab_study_variables(x, variable = "a")
-    expect_true(is.character(res))
-    expect_true(is.matrix(res))
-    expect_true(ncol(res) == 1L)
-    expect_equal(res[, 1L], c("a:1", "a:2", "a:3"))
-
-    res <- .mztab_study_variables(x, variable = c("a", "b"))
-    expect_true(is.character(res))
-    expect_true(is.matrix(res))
-    expect_true(ncol(res) == 2L)
-    expect_equal(res[, 1L], c("a:1", "a:2", "a:3"))
-    expect_equal(res[, 2L], c("b:1", "b:1", "b:2"))
-})
-
-test_that(".mztab_study_variable_entries works", {
-    x <- data.frame(a = 1:3, b = c(1, 1, 2))
-    res <- .mztab_study_variable_entries(x, variable = "a")
-    expect_true(is.character(res))
-    expect_true(is.matrix(res))
-    expect_true(ncol(res) == 2L)
-    expect_equal(unname(res[1, 1]), "study_variable[1]")
-    expect_equal(unname(res[2, 1]), "study_variable[1]-assay_refs")
-    expect_equal(unname(res[1, 2]), "a:1")
-    expect_equal(unname(res[2, 2]), "assay[1]")
-
-    res2 <- .mztab_study_variable_entries(x, variable = c("a", "b"))
-    expect_true(length(res2) > length(res))
-})
-
-test_that("storeResults,MzTabParam works", {
-    d <- tempdir()
-    p <- MzTabParam(studyId = "test_study", path = d,
-                    sampleDataColumn = "sample_index",
-                    optionalFeatureColumns = "peakidx")
-    storeResults(faahko, p)
-    expect_true(file.exists(file.path(d, "test_study.mztab")))
-    res <- readLines(file.path(d, "test_study.mztab"))
-    expect_true(length(res) > 0L)
-    expect_true(length(grep("^MTD", res)) > 0)
-    expect_true(length(grep("^SML", res)) > 0)
-    expect_true(length(grep("^SMF", res)) > 0)
-    ## Check for empty lines
-    expect_true(length(grep(c("^MTD|SML|SMF"), res, invert = TRUE)) == 2)
-})
diff --git a/tests/testthat/test_do_adjustRtime-functions.R b/tests/testthat/test_do_adjustRtime-functions.R
index 1f90ec845..2d36e1014 100644
--- a/tests/testthat/test_do_adjustRtime-functions.R
+++ b/tests/testthat/test_do_adjustRtime-functions.R
@@ -293,13 +293,16 @@ test_that(".match_reference_anchors works", {
                rt = c(100, 150.1, 190, 190, 190, 192))
     b <- cbind(mz = c(200.2, 232, 233.1, 234),
                rt = c(150, 190.4, 193, 240))
+    rownames(a) <- rep("a", nrow(a))
+    rownames(b) <- rep("b", nrow(b))
 
     res <- .match_reference_anchors(a, b)
     expect_true(is.data.frame(res))
-    expect_equal(colnames(res), c("ref", "obs"))
+    expect_equal(colnames(res), c("ref", "obs", "chromPeaksId"))
     expect_true(nrow(res) == 1L)
     expect_equal(res$ref, 193.0)
     expect_equal(res$obs, 190.0)
+    expect_equal(res$chromPeaksId, "a")
 
     ## no matches:
     res <- .match_reference_anchors(a, b, tolerance = 0, toleranceRt = 0)
@@ -311,7 +314,7 @@ test_that(".match_reference_anchors works", {
     ## rows 5 and 6 from `a` match row 3 from `b`
     res <- .match_reference_anchors(a, b, tolerance = 0.1, toleranceRt = 52)
     expect_true(is.data.frame(res))
-    expect_equal(colnames(res), c("ref", "obs"))
+    expect_equal(colnames(res),c("ref", "obs", "chromPeaksId"))
     expect_equal(res$ref, 190.4)
     expect_equal(res$obs, 190.0)
 
@@ -320,7 +323,7 @@ test_that(".match_reference_anchors works", {
     ## `b` and should thus not be reported.
     res <- .match_reference_anchors(a, b, tolerance = 0.1, toleranceRt = 5)
     expect_true(is.data.frame(res))
-    expect_equal(colnames(res), c("ref", "obs"))
+    expect_equal(colnames(res), c("ref", "obs", "chromPeaksId"))
     expect_equal(res$ref, c(150, 190.4))
     expect_equal(res$obs, c(150.1, 190.0))
 
@@ -328,7 +331,7 @@ test_that(".match_reference_anchors works", {
     ## with row 3 in `b`.
     res <- .match_reference_anchors(a, b, tolerance = 0.1, toleranceRt = 2)
     expect_true(is.data.frame(res))
-    expect_equal(colnames(res), c("ref", "obs"))
+    expect_equal(colnames(res), c("ref", "obs", "chromPeaksId"))
     expect_equal(res$ref, c(150, 190.4, 193.0))
     expect_equal(res$obs, c(150.1, 190.0, 192.0))
 })

From 89f17f0fc6c7410beb64d186752d5d2da1d9d659 Mon Sep 17 00:00:00 2001
From: Philippine Louail <127301965+philouail@users.noreply.github.com>
Date: Tue, 1 Oct 2024 22:07:27 +0200
Subject: [PATCH 5/9] removing MztabParam

---
 R/MzTabParam.R    | 416 ----------------------------------------------
 man/MzTabParam.Rd | 103 ------------
 2 files changed, 519 deletions(-)
 delete mode 100644 R/MzTabParam.R
 delete mode 100644 man/MzTabParam.Rd

diff --git a/R/MzTabParam.R b/R/MzTabParam.R
deleted file mode 100644
index 0b80eafc0..000000000
--- a/R/MzTabParam.R
+++ /dev/null
@@ -1,416 +0,0 @@
-#' @title Store contents of an `XcmsExperiment` objects as a .mztabm file
-#'
-#' @name MzTabParam
-#'
-#' @export
-#'
-#' @family xcms result export formats.
-#'
-#' @description
-#' The `MzTabParam` class and method enable users to save an `XcmsExperiment`
-#' object as a mzTabm format. Mainly the metadata (MTD) and Small molecule
-#' feature (SMF) tables will represent the `XcmsExperiment`. The small molecule
-#' summary section (SML) will be filled with `null` values as no annotation and
-#' identification of compound is performed in `xcms`.
-#'
-#' This `param` class and method are part of the possible dispatch of the
-#' generic function `storeResults`. The file will be created by calling
-#' `storeResults`. If the file already exists, it will get overwritten.
-#'
-#' @param studyId `character` Will be both the `filename` of the object saved in
-#' .mztabm format and the `mzTab-ID` in the file.
-#'
-#' @param polarity `character` Describes the polarity of the experiment. Two
-#' inputs are possible, "positive" (default) or "negative".
-#'
-#' @param sampleDataColumn `character` strings corresponding to the column name(s)
-#' of the `sampleData()` of the `XcmsExperiment` object with the different
-#' *variables* of the experiment, for example it could be *"phenotype"*,
-#' *"sample_type"*, etc...
-#'
-#' @param path `character(1)` Define where the file is going to be stored. The
-#' default will be `tempdir()`.
-#'
-#' @param optionalFeatureColumns Optional columns from `featureDefinitions`
-#' that should be exported too. For example it could be *"peakidx*,
-#' *"npeaks"*, etc...
-#'
-#' @slot dots `list` Correspond to any optional parameters to be passed
-#' to the `featureValues` function. (e.g. parameters `method` or `value`).
-#'
-#' @inheritParams storeResults
-#'
-#' @return for `MzTabParam`: a `MzTabParam` class. `storeResults` does
-#' not return anything but saves the object as a .mztabm file.
-#'
-#' @note
-#' This function was build so that the output fit the recommendation of mztab-m
-#' file format. These can be found here:
-#' (http://hupo-psi.github.io/mzTab/2_0-metabolomics-release/mzTab_format_specification_2_0-M_release.html)
-#'
-#' @references
-#'
-#' Hoffmann N, Rein J, Sachsenberg T, Hartler J, Haug K, Mayer G, Alka O,
-#' Dayalan S, Pearce JTM, Rocca-Serra P, Qi D, Eisenacher M, Perez-Riverol Y,
-#' Vizcaino JA, Salek RM, Neumann S, Jones AR. mzTab-M: A Data Standard for
-#' Sharing Quantitative Results in Mass Spectrometry Metabolomics. Anal Chem.
-#' 2019 Mar 5;91(5):3302-3310. doi: 10.1021/acs.analchem.8b04310. Epub 2019 Feb
-#' 13. PMID: 30688441; PMCID: PMC6660005.
-#'
-#' @author Philippine Louail, Johannes Rainer
-#'
-#' @examples
-#' ## Load a test data set with detected peaks, of class `XcmsExperiment`
-#' test_xcms <- loadXcmsData()
-#'
-#' ## Define param
-#' param <- MzTabParam(studyId = "test",
-#'                     polarity = "positive",
-#'                     sampleDataColumn = "sample_type")
-#'
-#' ## Save as a .mzTabm file
-#' storeResults(test_xcms, param)
-#'
-NULL
-
-#' @noRd
-setClass("MzTabParam",
-         slots = c(studyId = "character",
-                   polarity = "character",
-                   sampleDataColumn = "character",
-                   path = "character",
-                   optionalFeatureColumns = "character",
-                   dots = "list"
-                   ),
-         contains = "Param",
-         prototype = prototype(
-             studyId = character(),
-             polarity =  character(),
-             sampleDataColumn = character(),
-             path = character(),
-             optionalFeatureColumns = character(),
-             dots = list()
-         ),
-         validity = function(object) {
-             msg <- NULL
-             if(length(object@studyId) != 1)
-                msg <- c("'studyId' has to be a character string of length 1")
-             if(length(object@polarity) != 1)
-                 msg <- c(msg, "'polarity' has to be a character string of length 1")
-             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
-#'
-#' @export
-MzTabParam <- function(studyId = character(),
-                       polarity = c("positive", "negative"),
-                       sampleDataColumn = character(),
-                       path = tempdir(),
-                       optionalFeatureColumns = character(), ...) {
-    polarity <- match.arg(polarity)
-    new("MzTabParam", studyId = studyId, polarity = polarity,
-        sampleDataColumn = sampleDataColumn, path = path,
-        optionalFeatureColumns = optionalFeatureColumns, dots = list(...))
-}
-
-#' @rdname MzTabParam
-setMethod("storeResults",
-          signature(object = "XcmsExperiment",
-                    param = "MzTabParam"),
-          function(object, param){
-              if(!param@sampleDataColumn %in% colnames(sampleData(object)))
-                  stop("'sampleDataColumn' has to correspond to column names",
-                  "of the sampleData() table")
-              if(length(param@optionalFeatureColumns) != 0)
-                  if(!param@optionalFeatureColumns %in% colnames(featureDefinitions(object)))
-                      stop("'optionalFeatureColumns' have to correspond to",
-                      "column names of the featureDefinitions() table")
-
-              var_list <- unique(.mztab_study_variables(sampleData(object),
-                                                        param@sampleDataColumn))
-              fl <- file.path(param@path, paste0(param@studyId, ".mztab"))
-              if (file.exists(fl)) {
-                  warning("File ", basename(fl), " already exists. ",
-                          "Will overwrite.")
-                  file.remove(fl)
-              }
-              con <- file(fl, open = "at")
-              on.exit(close(con))
-
-              mtd <- .mztab_metadata(object, study_id = param@studyId,
-                                     polarity = param@polarity,
-                                     col_phenotype = param@sampleDataColumn)
-              .mztab_export(mtd, con)
-              writeLines("", con)
-
-              sml <- .mztab_small_molecule_summary(n_sample = length(object),
-                                                   var_list = var_list)
-              .mztab_export(sml, con)
-              writeLines("", con)
-
-              smf <- do.call(.mztab_small_molecule_feature,
-                             c(list(object = object,
-                                    opt_columns = param@optionalFeatureColumns),
-                                    param@dots))
-              .mztab_export(smf, con)
-          })
-
-
-### Helper functions
-
-#' @description
-#'
-#' Create the metadata `matrix` (MTD). Use the .MTD static object as a basis.
-#'
-#' @noRd
-.mztab_metadata <- function(object, study_id, polarity, col_phenotype) {
-    n_sample <- length(object)
-    seq_sample <- seq_len(n_sample)
-    base <- .MTD
-    base[base == "replace_id"]  <- study_id
-    msrun <- cbind(
-        name = paste0("ms_run[", seq_sample, "]-location"),
-        value = paste0("file:///", unlist(gsub(" ", "",fileNames(object)))),
-        order = .prefix_zero(seq_sample)
-    )
-    if (polarity == "positive") {
-        pol <- cbind(
-            name = paste0("ms_run[", seq_sample, "]-scan_polarity[1]"),
-            value = "[MS, MS:1000130, positive scan, ]",
-            order = .prefix_zero(seq_sample))
-    } else {
-        pol <- cbind(
-            name = paste0("ms_run[", seq_sample, "]-scan_polarity[1]"),
-            value = "[MS, MS:1000129, negative scan, ]",
-            order = .prefix_zero(seq_sample))
-    }
-    msrun <- rbind(msrun, pol)
-    msrun <- msrun[order(msrun[, "order"]), c("name", "value")]
-
-    assay <- cbind(
-        name = paste0("assay[", seq_sample, "]"),
-        value = paste(seq_sample, "assay"),
-        order = .prefix_zero(seq_sample)
-    )
-    assay_ref <- cbind(
-        name = paste0("assay[", seq_sample, "]-ms_run_ref"),
-        value = paste0("ms_run[", seq_sample, "]"),
-        order = .prefix_zero(seq_sample)
-    )
-    assay <- rbind(assay, assay_ref)
-    assay <- assay[order(assay[, "order"]), c("name", "value")]
-
-    var <- .mztab_study_variable_entries(sampleData(object), col_phenotype)
-
-    mtd <- rbind(
-        base[1:4, ],
-        msrun,
-        assay,
-        var,
-        base[5:nrow(base), ]
-    )
-    mtd <- cbind(id = "MTD", mtd)
-
-    gsub("\\\\", "/", mtd)
-}
-
-#' @description
-#'
-#' Create the *empty* small molecule summary (SML) `matrix`.
-#' Use the .SML static object as a basis
-#'
-#' @noRd
-#'
-#' @examples
-#'
-#' .mztab_small_molecule_summary(5, c(1, 2, 3))
-.mztab_small_molecule_summary <- function(n_sample, var_list) {
-    sml <- c(.SML, paste0("abundance_assay[", seq_len(n_sample) ,"]"),
-             paste0("abundance_study_variable[",
-                    seq_len(length(var_list)) ,"]"),
-             paste0("abundance_variation_study_variable[",
-                    seq_len(length(var_list)) ,"]"))
-    rbind(sml, c("SML", "1", rep("null", length(sml) - 2L)))
-}
-
-#' @description
-#'
-#' Create the small molecule feature (SMF) `matrix` One row is one feature
-#' defined in xcms. Use the .SMF static object.
-#' object as a basis.
-#'read
-#' @noRd
-#'
-#' @param object `XcmsExperiment`.
-#'
-#' @param opt_columns `character` defining optional columns in
-#'     `featureDefinitions` that should be exported too.
-#'
-#' @param ... optional parameters for the `featureValues` call.
-.mztab_small_molecule_feature <- function(object, opt_columns = character(),
-                                          ...) {
-    fts <- featureDefinitions(object)
-    smf <- matrix(data = "null", ncol = length(.SMF), nrow = nrow(fts),
-                  dimnames = list(character(), .SMF))
-    smf[, "SFH"] <- "SMF"
-    smf[, "SMF_ID"] <- seq_len(nrow(fts))
-    smf[, "exp_mass_to_charge"] <- as.character(fts$mzmed, digits = 18)
-    smf[, "retention_time_in_seconds"] <- as.character(fts$rtmed, digits = 15)
-    smf[, "retention_time_in_seconds_start"] <- as.character(fts$rtmin,
-                                                             digits = 15)
-    smf[, "retention_time_in_seconds_end"] <- as.character(fts$rtmax,
-                                                           digits = 15)
-
-    fvals <- featureValues(object, ...)
-    colnames(fvals) <- paste0("abundance_assay[", seq_len(ncol(fvals)), "]")
-    fvals <- apply(fvals, 2L, as.character, digits = 15)
-    fvals[is.na(fvals)] <- "null"
-
-    smf <- cbind(smf, fvals)
-
-    if (length(opt_columns)) {
-        tmp <- do.call(
-            cbind, lapply(opt_columns,
-                          function(z) {
-                              if (z == "peakidx") {
-                                  vapply(fts[, z], paste0, character(1),
-                                         collapse = "| ")
-                              } else as.character(fts[, z], digits = 15)
-                          }))
-        colnames(tmp) <- paste0("opt_", opt_columns)
-        smf <- cbind(smf, tmp)
-    }
-    smf <- rbind(colnames(smf), smf)
-    unname(smf)
-}
-
-#' @description
-#'
-#' Define the `character` vector with all study variables.
-#'
-#' @param x `data.frame` with sample annotations
-#'
-#' @param variable `character` with the column name(s) containing the study
-#'     variables.
-#'
-#' @return `character` with the study variables, being a concatenation of
-#'     the column name `"|"` and the value of the variable.
-#'
-#' @noRd
-#'
-#' @examples
-#'
-#' x <- data.frame(sex = c("male", "female", "female", "male", "male"),
-#'                 group = c("case", "case", "control", "case", "control"))
-#'
-#' .mztab_study_variables(x, variable = c("sex", "group"))
-#'
-#' .mztab_study_variables(x, "sex")
-.mztab_study_variables <- function(x = data.frame(), variable = character(),
-                                   sep = ":") {
-    do.call(cbind, lapply(variable, function(z) paste0(z, sep, x[, z])))
-}
-
-#' @description
-#'
-#' Create a `matrix` with the *study_variable* metadata content based.
-#'
-#' @param x `data.frame` representing the `sampleData` of the `MsExperiment`.
-#'
-#' @param variable `character` defining the columns in `x` containing the
-#'     sample variables.
-#'
-#' @return `character` `matrix` (two columns) with the result.
-#'
-#' @noRd
-#'
-#' @examples
-#'
-#' .mztab_study_variable_entries(x, "sex")
-#'
-#' .mztab_study_variable_entries(x, c("group", "sex"))
-.mztab_study_variable_entries <- function(x, variable, sep = "| ") {
-    svar <- .mztab_study_variables(x, variable)
-    unique_svar <- unique(as.vector(svar))
-    res <- matrix(character(), ncol = 2, nrow = 0,
-                  dimnames = list(character(), c("name", "value")))
-    for (i in seq_along(unique_svar)) {
-        idx <- which(svar == unique_svar[i], arr.ind = TRUE)
-        res <- rbind(
-            res,
-            matrix(ncol = 2,
-            c(paste0("study_variable[", i, "]"),
-              paste0("study_variable[", i, "]-description"),
-              paste0("study_variable[", i, "]-assay_refs"),
-              paste0(unique_svar[i]),
-              paste0("Sample in column ", unique_svar[i]), #either this or <to be filled>
-              paste0("assay[", idx[, "row"], "]", collapse = sep)
-              )))
-    }
-    res
-}
-
-#' @noRd
-.prefix_zero <- function(x) {
-    sprintf(paste0("%0", ceiling(log10(max(x) + 1)), "d"), x)
-}
-
-#' @noRd
-.mztab_export <- function(x, con) {
-    x <- apply(x, 1L, paste0, collapse = "\t")
-    writeLines(x, con)
-}
-
-### Static objects
-
-.MTD <- cbind(
-    name = c("mzTab-version",
-             "mzTab-ID",
-             "software[1]",
-             "quantification_method",
-             "cv[1]-label",
-             "cv[1]-full_name",
-             "cv[1]-version",
-             "cv[1]-uri",
-             "cv[2]-label",
-             "cv[2]-full_name",
-             "cv[2]-version",
-             "cv[2]-uri",
-             "database[1]",
-             "database[1]-prefix",
-             "database[1]-version",
-             "database[1]-uri",
-             "small_molecule_feature-quantification_unit"),
-    value = c("2.0.0-M",
-              "replace_id",
-              "[MS, MS:1001582, XCMS, 3.1.1]",
-              "[MS, MS:1001834, LC-MS label-free quantitation analysis, ]",
-              "MS",
-              "PSI-MS controlled vocabulary",
-              "4.1.138",
-              "https://raw.githubusercontent.com/HUPO-PSI/psi-ms-CV/master/psi-ms.obo",
-              "PRIDE",
-              "PRIDE PRoteomics IDEntifications (PRIDE) database controlled vocabulary",
-              "16:10:2023 11:38",
-              "https://www.ebi.ac.uk/ols/ontologies/pride",
-              "[,, \"no database\", null ]",
-              "null",
-              "Unknown",
-              "null",
-              "[PRIDE, PRIDE:0000330, Arbitrary quantification unit, ]"))
-
-.SML <- c("SMH", "SML_ID","SMF_ID_REFS", "database_identifier",
-          "chemical_formula", "smiles", "inchi", "chemical_name",
-          "uri", "theoretical_neutral_mass", "adduct_ions", "reliability",
-          "best_id_confidence_measure", "best_id_confidence_value")
-
-.SMF <- c("SFH", "SMF_ID","SME_ID_REFS", "SME_ID_REF_ambiguity_code",
-          "adduct_ion", "isotopomer", "exp_mass_to_charge", "charge",
-          "retention_time_in_seconds", "retention_time_in_seconds_start",
-          "retention_time_in_seconds_end")
-
diff --git a/man/MzTabParam.Rd b/man/MzTabParam.Rd
deleted file mode 100644
index 9c0591332..000000000
--- a/man/MzTabParam.Rd
+++ /dev/null
@@ -1,103 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/MzTabParam.R
-\name{MzTabParam}
-\alias{MzTabParam}
-\alias{storeResults,XcmsExperiment,MzTabParam-method}
-\title{Store contents of an `XcmsExperiment` objects as a .mztabm file}
-\usage{
-MzTabParam(
-  studyId = character(),
-  polarity = c("positive", "negative"),
-  sampleDataColumn = character(),
-  path = tempdir(),
-  optionalFeatureColumns = character(),
-  ...
-)
-
-\S4method{storeResults}{XcmsExperiment,MzTabParam}(object, param)
-}
-\arguments{
-\item{studyId}{`character` Will be both the `filename` of the object saved in
-.mztabm format and the `mzTab-ID` in the file.}
-
-\item{polarity}{`character` Describes the polarity of the experiment. Two
-inputs are possible, "positive" (default) or "negative".}
-
-\item{sampleDataColumn}{`character` strings corresponding to the column name(s)
-of the `sampleData()` of the `XcmsExperiment` object with the different
-*variables* of the experiment, for example it could be *"phenotype"*,
-*"sample_type"*, etc...}
-
-\item{path}{`character(1)` Define where the file is going to be stored. The
-default will be `tempdir()`.}
-
-\item{optionalFeatureColumns}{Optional columns from `featureDefinitions`
-that should be exported too. For example it could be *"peakidx*,
-*"npeaks"*, etc...}
-
-\item{...}{Optional parameters.}
-
-\item{object}{\code{MsExperiment} or \code{XcmsExperiment} The data object that needs
-to be saved.}
-
-\item{param}{The parameter object selecting and configuring the format for
-saving. It can be one of the following classes: \code{\link{RDataParam}},
-\code{\link{PlainTextParam}}, or \code{\link{MzTabParam}}.}
-}
-\value{
-for `MzTabParam`: a `MzTabParam` class. `storeResults` does
-not return anything but saves the object as a .mztabm file.
-}
-\description{
-The `MzTabParam` class and method enable users to save an `XcmsExperiment`
-object as a mzTabm format. Mainly the metadata (MTD) and Small molecule
-feature (SMF) tables will represent the `XcmsExperiment`. The small molecule
-summary section (SML) will be filled with `null` values as no annotation and
-identification of compound is performed in `xcms`.
-
-This `param` class and method are part of the possible dispatch of the
-generic function `storeResults`. The file will be created by calling
-`storeResults`. If the file already exists, it will get overwritten.
-}
-\section{Slots}{
-
-\describe{
-\item{\code{dots}}{`list` Correspond to any optional parameters to be passed
-to the `featureValues` function. (e.g. parameters `method` or `value`).}
-}}
-
-\note{
-This function was build so that the output fit the recommendation of mztab-m
-file format. These can be found here:
-(http://hupo-psi.github.io/mzTab/2_0-metabolomics-release/mzTab_format_specification_2_0-M_release.html)
-}
-\examples{
-## Load a test data set with detected peaks, of class `XcmsExperiment`
-test_xcms <- loadXcmsData()
-
-## Define param
-param <- MzTabParam(studyId = "test",
-                    polarity = "positive",
-                    sampleDataColumn = "sample_type")
-
-## Save as a .mzTabm file
-storeResults(test_xcms, param)
-
-}
-\references{
-Hoffmann N, Rein J, Sachsenberg T, Hartler J, Haug K, Mayer G, Alka O,
-Dayalan S, Pearce JTM, Rocca-Serra P, Qi D, Eisenacher M, Perez-Riverol Y,
-Vizcaino JA, Salek RM, Neumann S, Jones AR. mzTab-M: A Data Standard for
-Sharing Quantitative Results in Mass Spectrometry Metabolomics. Anal Chem.
-2019 Mar 5;91(5):3302-3310. doi: 10.1021/acs.analchem.8b04310. Epub 2019 Feb
-13. PMID: 30688441; PMCID: PMC6660005.
-}
-\seealso{
-Other xcms result export formats.: 
-\code{\link{PlainTextParam}},
-\code{\link{RDataParam}}
-}
-\author{
-Philippine Louail, Johannes Rainer
-}
-\concept{xcms result export formats.}

From c55523c3a9d00697b555f97b650cf32b7b595aee Mon Sep 17 00:00:00 2001
From: Philippine Louail <127301965+philouail@users.noreply.github.com>
Date: Wed, 2 Oct 2024 10:05:59 +0200
Subject: [PATCH 6/9] Update check-bioc.yml

---
 .github/workflows/check-bioc.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/check-bioc.yml b/.github/workflows/check-bioc.yml
index 8af610887..7da178a3a 100644
--- a/.github/workflows/check-bioc.yml
+++ b/.github/workflows/check-bioc.yml
@@ -222,7 +222,7 @@ jobs:
           rcmdcheck::rcmdcheck(
               args = c("--no-build-vignettes", "--no-manual", "--timings"),
               build_args = c("--no-manual", "--no-resave-data"),
-              error_on = "warning",
+              error_on = "error",
               check_dir = "check"
           )
         shell: Rscript {0}

From 9cd1ebd9776f0818896ef72755e5615e6e48c445 Mon Sep 17 00:00:00 2001
From: Philippine Louail <127301965+philouail@users.noreply.github.com>
Date: Thu, 3 Oct 2024 09:22:00 +0200
Subject: [PATCH 7/9] bump version

---
 DESCRIPTION | 2 +-
 NEWS.md     | 9 +++++++++
 2 files changed, 10 insertions(+), 1 deletion(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index a9c46263e..6fd200747 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,5 +1,5 @@
 Package: xcms
-Version: 4.3.3
+Version: 4.3.4
 Title: LC-MS and GC-MS Data Analysis
 Description: Framework for processing and visualization of chromatographically
     separated and single-spectra mass spectral data. Imports from AIA/ANDI NetCDF,
diff --git a/NEWS.md b/NEWS.md
index 1a47aa96e..536bc58e5 100644
--- a/NEWS.md
+++ b/NEWS.md
@@ -1,5 +1,14 @@
 # xcms 4.3
 
+## Changes in version 4.3.4
+
+- Small update to the `matchLamaChromPeaks()` function to get the chromPeaksId
+  of the chromPeaks matched with Lamas. 
+- Small fix to the .yml file for the github actions, so they do not crash on 
+  warnings.
+
+
+
 ## Changes in version 4.3.3
 
 - Fix issue #755: `chromatogram()` with `msLevel = 2` fails to extract

From 324bb462699b123fbec2398f7e9ee05b332c2e7f Mon Sep 17 00:00:00 2001
From: J Wokaty <jennifer.wokaty@sph.cuny.edu>
Date: Tue, 29 Oct 2024 09:24:25 -0400
Subject: [PATCH 8/9] bump x.y.z version to even y prior to creation of
 RELEASE_3_20 branch

---
 DESCRIPTION | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index a9c46263e..685a54874 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,5 +1,5 @@
 Package: xcms
-Version: 4.3.3
+Version: 4.4.0
 Title: LC-MS and GC-MS Data Analysis
 Description: Framework for processing and visualization of chromatographically
     separated and single-spectra mass spectral data. Imports from AIA/ANDI NetCDF,

From 3c1702c2cc34b5fa05386b7bcedbbe7360cbe757 Mon Sep 17 00:00:00 2001
From: J Wokaty <jennifer.wokaty@sph.cuny.edu>
Date: Tue, 29 Oct 2024 09:24:25 -0400
Subject: [PATCH 9/9] bump x.y.z version to odd y following creation of
 RELEASE_3_20 branch

---
 DESCRIPTION | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index 685a54874..154df8389 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,5 +1,5 @@
 Package: xcms
-Version: 4.4.0
+Version: 4.5.0
 Title: LC-MS and GC-MS Data Analysis
 Description: Framework for processing and visualization of chromatographically
     separated and single-spectra mass spectral data. Imports from AIA/ANDI NetCDF,