{
  "_id": "6a1ac3601d7bb097a09da406",
  "Package": "metabCombiner",
  "Version": "1.23.0",
  "Date": "2024-05-23",
  "Title": "Method for Combining LC-MS Metabolomics Feature Measurements",
  "Authors@R": "c(\nperson(\"Hani\", \"Habra\", email = \"hhabra1@gmail.com\",role = c(\"aut\",\"cre\")),\nperson(\"Alla\", \"Karnovsky\", email = \"akarnovs@med.umich.edu\", role = \"ths\"))",
  "License": "GPL-3",
  "Description": "This package aligns LC-HRMS metabolomics datasets acquired\nfrom biologically similar specimens analyzed under similar, but\nnot necessarily identical, conditions. Peak-picked and simply\naligned metabolomics feature tables (consisting of m/z, rt, and\nper-sample abundance measurements, plus optional identifiers &\nadduct annotations) are accepted as input. The package outputs\na combined table of feature pair alignments, organized into\ngroups of similar m/z, and ranked by a similarity score. Input\ntables are assumed to be acquired using similar (but not\nnecessarily identical) analytical methods.",
  "BugReports": "https://www.github.com/hhabra/metabCombiner/issues",
  "NeedsCompilation": "yes",
  "RoxygenNote": "7.1.1",
  "Encoding": "UTF-8",
  "Collate": "'adjustData.R' 'batchCombine.R' 'calcScores.R' 'check_pars.R'\n'classes.R' 'combinerCheck.R' 'compare_strings.R' 'data.R'\n'detectFields.R' 'evaluateParams.R' 'fit_model.R' 'form.R'\n'generics.R' 'labelRows.R' 'metabCombine.R' 'metabCombiner.R'\n'metabCombiner_package_doc.R' 'metabData.R'\n'methods-featdata.R' 'methods-metabCombiner.R'\n'methods-metabData.R' 'mzGroup.R' 'params.R' 'plot_fit.R'\n'resolveRows.R' 'selectAnchors.R' 'updateTables.R'\n'write2file.R' 'zzz.R'",
  "VignetteBuilder": "knitr",
  "biocViews": "Software, MassSpectrometry, Metabolomics",
  "LazyData": "false",
  "Config/pak/sysreqs": "libicu-dev",
  "Repository": "https://bioc.r-universe.dev",
  "Date/Publication": "2026-04-28 12:54:08 UTC",
  "RemoteUrl": "https://github.com/bioc/metabCombiner",
  "RemoteRef": "HEAD",
  "RemoteSha": "24679206185bf2e4ab000a1b5dcc22a127637c12",
  "Packaged": {
    "Date": "2026-05-30 07:40:21 UTC",
    "User": "root"
  },
  "Author": "Hani Habra [aut, cre],\nAlla Karnovsky [ths]",
  "Maintainer": "Hani Habra <hhabra1@gmail.com>",
  "MD5sum": "6b048a841b2141421fcdf04c5daf75e5",
  "_user": "bioc",
  "_type": "src",
  "_file": "metabCombiner_1.23.0.tar.gz",
  "_fileid": "b2e15c415a4d9d844907db07043953d5e4414fe4966690fb0b2c4abfe2ee8d1e",
  "_filesize": 2801587,
  "_sha256": "b2e15c415a4d9d844907db07043953d5e4414fe4966690fb0b2c4abfe2ee8d1e",
  "_created": "2026-05-30T07:40:21.000Z",
  "_published": "2026-05-30T11:00:48.206Z",
  "_jobs": [
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  "_bioccheck": {
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    "warning": 2,
    "note": 13
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  "_buildurl": "https://github.com/r-universe/bioc/actions/runs/26678221644",
  "_status": "success",
  "_host": "GitHub-Actions",
  "_upstream": "https://github.com/bioc/metabCombiner",
  "_commit": {
    "id": "24679206185bf2e4ab000a1b5dcc22a127637c12",
    "author": "A Wokaty <andres.wokaty@sph.cuny.edu>",
    "committer": "A Wokaty <andres.wokaty@sph.cuny.edu>",
    "message": "bump x.y.z version to odd y following creation of RELEASE_3_23 branch\n",
    "time": 1777380848
  },
  "_maintainer": {
    "name": "Hani Habra",
    "email": "hhabra1@gmail.com",
    "login": "hhabra",
    "description": "PhD in Computational Medicine & Bioinformatics. ",
    "uuid": 8129799
  },
  "_distro": "noble",
  "_registered": true,
  "_dependencies": [
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      "package": "R",
      "version": ">= 4.0",
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      "package": "dplyr",
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      "package": "stats",
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    {
      "package": "utils",
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    },
    {
      "package": "rlang",
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    {
      "package": "graphics",
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    {
      "package": "matrixStats",
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      "package": "tidyr",
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  ],
  "_owner": "bioc",
  "_selfowned": true,
  "_usedby": 0,
  "_updates": [
    {
      "week": "2025-44",
      "n": 2
    },
    {
      "week": "2026-18",
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  ],
  "_tags": [],
  "_bioc": [
    {
      "branch": "devel",
      "version": "1.23.0",
      "bioc": "3.24"
    },
    {
      "branch": "release",
      "version": "1.22.0",
      "bioc": "3.23"
    }
  ],
  "_topics": [
    "software",
    "massspectrometry",
    "metabolomics",
    "mass-spectrometry"
  ],
  "_stars": 13,
  "_contributors": [
    {
      "user": "hhabra",
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      "uuid": 8129799
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    "type": "organization",
    "name": "Bioconductor",
    "description": "Software for the analysis and comprehension of high-throughput genomic data"
  },
  "_downloads": {
    "count": 422,
    "source": "https://www.bioconductor.org/packages/stats/bioc/metabCombiner"
  },
  "_devurl": "https://github.com/hhabra/metabcombiner",
  "_searchresults": 13,
  "_rbuild": "4.6.0",
  "_assets": [
    "extra/citation.cff",
    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/contents.json",
    "extra/metabCombiner.html",
    "extra/NEWS.html",
    "extra/NEWS.txt",
    "extra/readme.html",
    "extra/readme.md",
    "manual.pdf"
  ],
  "_homeurl": "https://github.com/hhabra/metabcombiner",
  "_realowner": "bioc",
  "_cranurl": false,
  "_exports": [
    "adductData",
    "batchCombine",
    "calcScores",
    "calcScoresParam",
    "combineData",
    "combinedTable",
    "datasets",
    "evaluateParams",
    "featData",
    "filtered",
    "fit_gam",
    "fit_loess",
    "fitgamParam",
    "fitloessParam",
    "getAnchors",
    "getCoefficients",
    "getData",
    "getExtra",
    "getModel",
    "getSamples",
    "getStats",
    "idData",
    "labelRows",
    "labelRowsParam",
    "metabCombine",
    "metabCombiner",
    "metabData",
    "mzData",
    "mzFit",
    "mzfitParam",
    "nonmatched",
    "opts.duplicate",
    "plot",
    "plot_fit",
    "QData",
    "reduceTable",
    "reduceTableParam",
    "rtData",
    "selectAnchors",
    "selectAnchorsParam",
    "updateTables",
    "write2file",
    "x",
    "xy",
    "y"
  ],
  "_datasets": [
    {
      "name": "metabBatches",
      "title": "Three LC-MS Metabolomics Batch Datasets",
      "object": "metabBatches",
      "file": "metabBatches.rda",
      "class": [
        "list"
      ],
      "fields": [],
      "table": true,
      "tojson": true
    },
    {
      "name": "plasma20",
      "title": "20 minute LC-MS Analysis of Human Plasma",
      "object": "plasma20",
      "file": "plasma20.rda",
      "class": [
        "data.frame"
      ],
      "fields": [
        "feature",
        "identity",
        "adduct",
        "mz",
        "rt",
        "CHEAR.20min.1",
        "CHEAR.20min.2",
        "CHEAR.20min.3",
        "CHEAR.20min.4",
        "CHEAR.20min.5",
        "Blank.20min.1",
        "Blank.20min.2",
        "POOL.20min.1",
        "POOL.20min.2",
        "POOL.20min.3",
        "POOL.20min.4",
        "POOL.20min.5",
        "RedCross.20min.1",
        "RedCross.20min.2",
        "RedCross.20min.3",
        "RedCross.20min.4",
        "RedCross.20min.5"
      ],
      "rows": 8910,
      "table": true,
      "tojson": true
    },
    {
      "name": "plasma30",
      "title": "30 minute LC-MS Analysis of Human Plasma",
      "object": "plasma30",
      "file": "plasma30.rda",
      "class": [
        "data.frame"
      ],
      "fields": [
        "feature",
        "identity",
        "adduct",
        "mz",
        "rt",
        "CHEAR.30min.1",
        "CHEAR.30min.2",
        "CHEAR.30min.3",
        "CHEAR.30min.4",
        "CHEAR.30min.5",
        "Blank.30min.1",
        "Blank.30min.2",
        "POOL.30min.1",
        "POOL.30min.2",
        "POOL.30min.3",
        "POOL.30min.4",
        "POOL.30min.5",
        "RedCross.30min.1",
        "RedCross.30min.2",
        "RedCross.30min.3",
        "RedCross.30min.4",
        "RedCross.30min.5"
      ],
      "rows": 8286,
      "table": true,
      "tojson": true
    }
  ],
  "_help": [
    {
      "page": "adductdata",
      "title": "Retrieve Adduct Annotations",
      "topics": [
        "adductData",
        "adductData,metabCombiner-method"
      ]
    },
    {
      "page": "adjustData",
      "title": "Process and Filter Metabolomics Feature Lists",
      "topics": [
        "adjustData"
      ]
    },
    {
      "page": "batchCombine",
      "title": "Stepwise Multi-batch LC-MS Alignment",
      "topics": [
        "batchCombine"
      ]
    },
    {
      "page": "calcScores",
      "title": "Compute Feature Similarity Scores",
      "topics": [
        "calcScores"
      ]
    },
    {
      "page": "calcScoresParam",
      "title": "List calcScores Defaults",
      "topics": [
        "calcScoresParam"
      ]
    },
    {
      "page": "combineData",
      "title": "Obtain All Feature Data",
      "topics": [
        "combineData",
        "combineData,metabCombiner-method"
      ]
    },
    {
      "page": "combinedTable",
      "title": "Obtain Feature Alignment Report",
      "topics": [
        "combinedTable",
        "combinedTable,metabCombiner-method"
      ]
    },
    {
      "page": "combinerCheck",
      "title": "Obtain Errors for metabCombiner Object Checks",
      "topics": [
        "combinerCheck"
      ]
    },
    {
      "page": "crossValFit",
      "title": "Cross Validation for Model Fits",
      "topics": [
        "crossValFit"
      ]
    },
    {
      "page": "datasets",
      "title": "Obtain Dataset IDs",
      "topics": [
        "datasets",
        "datasets,metabCombiner-method"
      ]
    },
    {
      "page": "detectFields",
      "title": "Detect metabData Input Columns",
      "topics": [
        "detectFields"
      ]
    },
    {
      "page": "evaluateParams",
      "title": "Evaluate Similarity Score Parameters",
      "topics": [
        "evaluateParams"
      ]
    },
    {
      "page": "featdata",
      "title": "Obtain Feature Metadata",
      "topics": [
        "featData",
        "featData,metabCombiner-method"
      ]
    },
    {
      "page": "filterAnchors",
      "title": "Filter Outlier Ordered Pairs",
      "topics": [
        "filterAnchors"
      ]
    },
    {
      "page": "filtered",
      "title": "Retrieve Filtered Features",
      "topics": [
        "filtered",
        "filtered,metabData-method"
      ]
    },
    {
      "page": "filterRT",
      "title": "Filter Features by Retention Time Range",
      "topics": [
        "filterRT"
      ]
    },
    {
      "page": "fit_gam",
      "title": "Fit RT Projection Model With GAMs",
      "topics": [
        "fit_gam"
      ]
    },
    {
      "page": "fit_loess",
      "title": "Fit RT Projection Model With LOESS",
      "topics": [
        "fit_loess"
      ]
    },
    {
      "page": "fitgamParam",
      "title": "List fit_gam Defaults",
      "topics": [
        "fitgamParam"
      ]
    },
    {
      "page": "fitloessParam",
      "title": "List fitLoess Defaults",
      "topics": [
        "fitloessParam"
      ]
    },
    {
      "page": "getAnchors",
      "title": "Get Ordered Retention Time Pairs",
      "topics": [
        "getAnchors",
        "getAnchors,metabCombiner-method"
      ]
    },
    {
      "page": "getCoefficients",
      "title": "Obtain Last-Used Score Coefficients",
      "topics": [
        "getCoefficients",
        "getCoefficients,metabCombiner-method"
      ]
    },
    {
      "page": "getData",
      "title": "Get Processed Dataset",
      "topics": [
        "getData",
        "getData,metabData-method"
      ]
    },
    {
      "page": "getExtra",
      "title": "Get Extra Data Column Names",
      "topics": [
        "getExtra",
        "getExtra,metabCombiner-method",
        "getExtra,metabData-method"
      ]
    },
    {
      "page": "getModel",
      "title": "Get Fitted RT Model",
      "topics": [
        "getModel",
        "getModel,metabCombiner-method"
      ]
    },
    {
      "page": "getSamples",
      "title": "Get Sample Names From metabCombiner or metabData Object",
      "topics": [
        "getSamples",
        "getSamples,metabCombiner-method",
        "getSamples,metabData-method"
      ]
    },
    {
      "page": "getStats",
      "title": "Get Object Statistics",
      "topics": [
        "getStats",
        "getStats,metabCombiner-method",
        "getStats,metabData-method"
      ]
    },
    {
      "page": "iddata",
      "title": "Retrieve Feature Identities",
      "topics": [
        "idData",
        "idData,metabCombiner-method"
      ]
    },
    {
      "page": "identityAnchorSelection",
      "title": "Select Matching Ids as Anchors",
      "topics": [
        "identityAnchorSelection"
      ]
    },
    {
      "page": "isCombinedTable",
      "title": "Determine 'combinedTable' Validity",
      "topics": [
        "isCombinedTable"
      ]
    },
    {
      "page": "isMetabCombiner",
      "title": "Determine if object is a valid metabCombiner object",
      "topics": [
        "isMetabCombiner"
      ]
    },
    {
      "page": "isMetabData",
      "title": "Determine validity of input metabData object",
      "topics": [
        "isMetabData"
      ]
    },
    {
      "page": "iterativeAnchorSelection",
      "title": "Iterative Selection of Ordered Pairs",
      "topics": [
        "iterativeAnchorSelection"
      ]
    },
    {
      "page": "labelRows",
      "title": "Annotate and Remove Report Rows",
      "topics": [
        "labelRows",
        "reduceTable"
      ]
    },
    {
      "page": "labelRowsParam",
      "title": "List labelRows & reduceTable Defaults",
      "topics": [
        "labelRowsParam",
        "reduceTableParam"
      ]
    },
    {
      "page": "metabBatches",
      "title": "Three LC-MS Metabolomics Batch Datasets",
      "topics": [
        "metabBatches"
      ]
    },
    {
      "page": "metabCombine",
      "title": "metabCombiner Wrapper Function",
      "topics": [
        "metabCombine"
      ]
    },
    {
      "page": "metabCombiner",
      "title": "Form a metabCombiner object.",
      "topics": [
        "metabCombiner"
      ]
    },
    {
      "page": "metabCombiner-class",
      "title": "'metabCombiner' Combined Metabolomics Dataset Class",
      "topics": [
        "metabCombiner-class"
      ]
    },
    {
      "page": "metabData",
      "title": "Constructor for the metabData object.",
      "topics": [
        "metabData"
      ]
    },
    {
      "page": "metabData-class",
      "title": "'metabData' Single Metabolomics Dataset Class",
      "topics": [
        "metabData-class"
      ]
    },
    {
      "page": "mzdata",
      "title": "Retrieve m/z Values",
      "topics": [
        "mzData",
        "mzData,metabCombiner-method"
      ]
    },
    {
      "page": "mzFit",
      "title": "Compute m/z Shift Model",
      "topics": [
        "mzFit"
      ]
    },
    {
      "page": "mzfitParam",
      "title": "Parameterize m/z Shift Model",
      "topics": [
        "mzfitParam"
      ]
    },
    {
      "page": "mzGroup",
      "title": "Binning of mass spectral features in m/z dimension",
      "topics": [
        "mzGroup"
      ]
    },
    {
      "page": "nonmatched",
      "title": "Get Nonmatched Features",
      "topics": [
        "nonmatched",
        "nonmatched,metabCombiner-method"
      ]
    },
    {
      "page": "objective",
      "title": "Weight Parameter Objective Function",
      "topics": [
        "objective"
      ]
    },
    {
      "page": "opts.duplicate",
      "title": "Duplicate Feature Detection Parameters",
      "topics": [
        "opts.duplicate"
      ]
    },
    {
      "page": "plasma20",
      "title": "20 minute LC-MS Analysis of Human Plasma",
      "topics": [
        "plasma20"
      ]
    },
    {
      "page": "plasma30",
      "title": "30 minute LC-MS Analysis of Human Plasma",
      "topics": [
        "plasma30"
      ]
    },
    {
      "page": "plot_fit",
      "title": "Plot metabCombiner Fits",
      "topics": [
        "plot,metabCombiner,ANY-method",
        "plot_fit"
      ]
    },
    {
      "page": "Qdata",
      "title": "Retrieve Relative Abundance Values",
      "topics": [
        "QData",
        "QData,metabCombiner-method"
      ]
    },
    {
      "page": "resolveRows",
      "title": "Resolve Conflicting Alignment Subgroups",
      "topics": [
        "resolveRows"
      ]
    },
    {
      "page": "rtdata",
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