{
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  "Package": "RmzTabM",
  "Title": "R API for the mzTab-M Reference Implementation",
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  "Authors@R": "c(\nperson(given = \"Nils\",\nfamily = \"Hoffmann\",\nemail = \"nils.hoffmann@cebitec.uni-bielefeld.de\",\nrole = c(\"ctb\"),\ncomment = c(ORCID = \"0000-0002-6540-6875\")),\nperson(given = \"Steffen\",\nfamily = \"Neumann\",\nemail = \"sneumann@ipb-halle.de\",\nrole = c(\"ctb\"),\ncomment = c(ORCID = \"0000-0002-7899-7192\")),\nperson(given = \"Johannes\", family = \"Rainer\",\nemail = \"johannes.rainer@eurac.edu\",\nrole = c(\"aut\", \"cre\"),\ncomment = c(ORCID = \"0000-0002-6977-7147\")),\nperson(given = \"Philippine\", family = \"Louail\",\nemail = \"philippine.louail@eurac.edu\",\nrole = c(\"aut\"),\ncomment = c(ORCID = \"0009-0007-5429-6846\",\nfnd = \"European Union HORIZON-MSCA-2021 project Grant No. 101073062: HUMAN – Harmonising and Unifying Blood Metabolic Analysis Networks\")),\nperson(given = \"Gabriele\", family = \"Tomè\",\nemail = \"gabriele.tome@eurac.edu\",\nrole = c(\"aut\"),\ncomment = c(ORCID = \"0000-0002-3976-6068\",\nfnd = \"MetaRbolomics4Galaxy project (CUP: D53C25001030003) co-funded by the Autonomous Province of Bolzano under the Joint Projects South Tyrol–Germany 2025 program.\"))\n)",
  "Description": "The RmzTabM package provides functions to read and write\nfiles in the HUPO-PSI mzTab-M file format for reporting of\nresults from metabolomics and lipidomics experiments. This\npackage represents the reference implementation for mzTab-M\nimport/export for R. Core, low level functions allow to format\nand parse the individual sections of the mzTab-M format. These\nfunctions are designed to be re-used by other packages\nimplementing import/export of results in mzTab-M.",
  "Encoding": "UTF-8",
  "License": "Artistic-2.0",
  "URL": "https://github.com/RforMassSpectrometry/RmzTabM",
  "BugReports": "https://github.com/RforMassSpectrometry/RmzTabM/issues",
  "SystemRequirements": "pandoc, quarto",
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  "biocViews": "Infrastructure, MassSpectrometry, Metabolomics, Proteomics",
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  "Repository": "https://bioc.r-universe.dev",
  "Date/Publication": "2026-10-14 13:59:11 UTC",
  "RemoteUrl": "https://github.com/bioc/RmzTabM",
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  "NeedsCompilation": "no",
  "Packaged": {
    "Date": "2026-10-14 18:57:17 UTC",
    "User": "root"
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  "Author": "Nils Hoffmann [ctb] (ORCID: <https://orcid.org/0000-0002-6540-6875>),\nSteffen Neumann [ctb] (ORCID: <https://orcid.org/0000-0002-7899-7192>),\nJohannes Rainer [aut, cre] (ORCID:\n<https://orcid.org/0000-0002-6977-7147>),\nPhilippine Louail [aut] (ORCID:\n<https://orcid.org/0009-0007-5429-6846>, fnd: European Union\nHORIZON-MSCA-2021 project Grant No. 101073062: HUMAN – Harmonising\nand Unifying Blood Metabolic Analysis Networks),\nGabriele Tomè [aut] (ORCID: <https://orcid.org/0000-0002-3976-6068>,\nfnd: MetaRbolomics4Galaxy project (CUP: D53C25001030003) co-funded\nby the Autonomous Province of Bolzano under the Joint Projects\nSouth Tyrol–Germany 2025 program.)",
  "Maintainer": "Johannes Rainer <johannes.rainer@eurac.edu>",
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  "_created": "2026-10-14T18:57:17.000Z",
  "_published": "2026-10-14T19:20:21.433Z",
  "_buildurl": "https://github.com/r-universe/bioc/actions/runs/38618766737",
  "_status": "success",
  "_host": "GitHub-Actions",
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    "message": "Merge pull request #55 from rformassspectrometry/jomain\n\nSmall updates and documentation fixes",
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  "_exports": [
    "assayCols",
    "getMtdContact",
    "getMtdCv",
    "getMtdDatabase",
    "getMtdField",
    "getMtdInstrument",
    "getMtdProtocol",
    "isCvParameter",
    "makeSummarizedExperimentFromMzTabM",
    "msRunCols",
    "mtd",
    "mtdAssay",
    "mtdDefineStudyVariables",
    "mtdFields",
    "mtdFromSampleData",
    "mtdMsRun",
    "mtdSample",
    "mtdSkeleton",
    "mtdSort",
    "mtdStudyVariables",
    "mtdToSampleData",
    "MzTabM",
    "mzTabMValidator",
    "mzTabMValidator_download",
    "parseCvParameter",
    "readMzTabM",
    "sampleCols",
    "setMtdContact",
    "setMtdCv",
    "setMtdDatabase",
    "setMtdField",
    "setMtdInstrument",
    "setMtdProtocol",
    "sme",
    "smeCreate",
    "smeIdConfidenceMeasure",
    "smeSort",
    "smeSpectraRefValidator",
    "smf",
    "smfCols",
    "smfCreate",
    "smfSort",
    "sml",
    "smlAddStudyVariableColumns",
    "smlCreate",
    "smlSort",
    "writeMzTabM"
  ],
  "_datasets": [
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      "name": "se",
      "title": "Quantified LC-MS preprocessing result test data from Metabonaut",
      "object": "se",
      "file": "se.RData",
      "class": [
        "SummarizedExperiment"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    }
  ],
  "_help": [
    {
      "page": "MTD-export",
      "title": "Defining and exporting the mzTab-M metadata table",
      "topics": [
        "MTD-export"
      ]
    },
    {
      "page": "mtdAssay",
      "title": "mzTab-M _assay_ metadata information",
      "topics": [
        "mtdAssay"
      ]
    },
    {
      "page": "mtdFields",
      "title": "Prepare and format information for the mzTab-M metadata section",
      "topics": [
        "mtdFields"
      ]
    },
    {
      "page": "mtdFromSampleData",
      "title": "Create the mzTab-M MTD content from a sample data frame",
      "topics": [
        "assayCols",
        "msRunCols",
        "mtdFromSampleData",
        "sampleCols"
      ]
    },
    {
      "page": "mtdMsRun",
      "title": "mzTab-M _ms_run_ metadata fields",
      "topics": [
        "mtdMsRun"
      ]
    },
    {
      "page": "mtdSample",
      "title": "mzTab-M _sample_ metadata information",
      "topics": [
        "mtdSample"
      ]
    },
    {
      "page": "mtdSkeleton",
      "title": "Create a skeleton MTD section with general information",
      "topics": [
        "mtdSkeleton"
      ]
    },
    {
      "page": "mtdSort",
      "title": "Sort rows in a MTD matrix to match the expected order",
      "topics": [
        "mtdSort"
      ]
    },
    {
      "page": "mtdStudyVariables",
      "title": "mzTab-M _study variables_ metadata information",
      "topics": [
        "mtdDefineStudyVariables",
        "mtdStudyVariables"
      ]
    },
    {
      "page": "mtdToSampleData",
      "title": "Reconstruct a sample data frame from mzTab-M MTD content",
      "topics": [
        "mtdToSampleData"
      ]
    },
    {
      "page": "MzTabM",
      "title": "mzTab-M data container",
      "topics": [
        "mtd",
        "mtd,MzTabM-method",
        "MzTabM",
        "MzTabM,dfmatrix-method",
        "MzTabM,missing-method",
        "MzTabM-class",
        "sme",
        "sme,MzTabM-method",
        "smf",
        "smf,MzTabM-method",
        "sml",
        "sml,MzTabM-method"
      ]
    },
    {
      "page": "MzTabM-export",
      "title": "Export a mzTab-M 2.1 file",
      "topics": [
        "MzTabM-export",
        "writeMzTabM"
      ]
    },
    {
      "page": "MzTabM-import",
      "title": "Import a mzTab-M 2.1 file",
      "topics": [
        "MzTabM-import",
        "readMzTabM"
      ]
    },
    {
      "page": "mzTabMValidator",
      "title": "Validate an mzTab-M file using the official jmztabm-validator",
      "topics": [
        "mzTabMValidator"
      ]
    },
    {
      "page": "mzTabMValidator_download",
      "title": "Download the jmztabm-validator binary",
      "topics": [
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    },
    {
      "page": "parseCvParameter",
      "title": "Utility functions for CV parameters",
      "concept": [
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      "topics": [
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        "parseCvParameter"
      ]
    },
    {
      "page": "se",
      "title": "Quantified LC-MS preprocessing result test data from Metabonaut",
      "topics": [
        "se"
      ]
    },
    {
      "page": "setMtdContact",
      "title": "Add or Update contact Metadata of an mzTab-M MTD section",
      "topics": [
        "getMtdContact",
        "setMtdContact",
        "setMtdContact,dfmatrix-method",
        "setMtdContact,MzTabM-method"
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    },
    {
      "page": "setMtdCv",
      "title": "Add or Update Controlled Vocabularies (CV) Metadata of an mzTab-M MTD section",
      "topics": [
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        "setMtdCv",
        "setMtdCv,dfmatrix-method",
        "setMtdCv,MzTabM-method"
      ]
    },
    {
      "page": "setMtdDatabase",
      "title": "Add or Update Database Metadata of an mzTab-M MTD section",
      "topics": [
        "getMtdDatabase",
        "setMtdDatabase",
        "setMtdDatabase,dfmatrix-method",
        "setMtdDatabase,MzTabM-method"
      ]
    },
    {
      "page": "setMtdField",
      "title": "Add or Update a Metadata Field of an mzTab-M MTD section",
      "topics": [
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        "setMtdField",
        "setMtdField,dfmatrix-method",
        "setMtdField,MzTabM-method"
      ]
    },
    {
      "page": "setMtdInstrument",
      "title": "Add, update or get instrument metadata of an mzTab-M MTD section",
      "topics": [
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        "setMtdInstrument",
        "setMtdInstrument,dfmatrix-method",
        "setMtdInstrument,MzTabM-method"
      ]
    },
    {
      "page": "setMtdProtocol",
      "title": "Add or Update protocol Metadata of an mzTab-M MTD section",
      "topics": [
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        "setMtdProtocol",
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    {
      "page": "SME-export",
      "title": "Creating the mzTab-M Small Molecule (SME) Table",
      "topics": [
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        "smeCreate",
        "smeIdConfidenceMeasure",
        "smeSort",
        "smeSpectraRefValidator"
      ]
    },
    {
      "page": "SMF-export",
      "title": "Create the mzTab-M Small Molecule Feature (SMF) Table",
      "topics": [
        "SMF-export",
        "smfCreate",
        "smfSort"
      ]
    },
    {
      "page": "SML-export",
      "title": "Creating the mzTab-M Small Molecule (SML) Table",
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        "smlAddStudyVariableColumns",
        "smlCreate",
        "smlSort"
      ]
    },
    {
      "page": "SummarizedExperiment-mzTab-M",
      "title": "Create a mzTab-M file from a 'SummarizedExperiment' object",
      "topics": [
        "makeSummarizedExperimentFromMzTabM",
        "MzTabM,SummarizedExperiment-method",
        "smf,SummarizedExperiment-method",
        "smfCols",
        "SummarizedExperiment-mzTab-M"
      ]
    }
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      "filename": "rmztabm-api.html",
      "title": "The R API for the mzTab-M File Format",
      "engine": "quarto::html",
      "headings": [
        "Introduction",
        "Installation",
        "General information on the mzTab-M format",
        "R mzTab-M API",
        "High-level, user faced functions",
        "Get the Metabonaut result object",
        "Define the data set's metadata (MTD)",
        "Add feature abundance matrix (SMF)",
        "Completing the metadata content",
        "Export to an MTD+SMF mzTab-M file",
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        "Small Evidence (SME) Table",
        "General utility functions",
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      "created": "2025-12-09 12:36:14",
      "modified": "2026-10-14 13:59:11",
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