{
  "_id": "6a2126a6cd65a98ecbd21215",
  "Package": "MAIT",
  "Type": "Package",
  "Title": "Statistical Analysis of Metabolomic Data",
  "Version": "1.46.0",
  "Date": "09-06-2020",
  "Author": "Francesc Fernandez-Albert, Rafael Llorach, Cristina\nAndres-LaCueva, Alexandre Perera",
  "Maintainer": "Pol Sola-Santos <pol.soladelossantos@gmail.com>",
  "Description": "The MAIT package contains functions to perform end-to-end\nstatistical analysis of LC/MS Metabolomic Data. Special\nemphasis is put on peak annotation and in modular function\ndesign of the functions.",
  "biocViews": "ImmunoOncology, MassSpectrometry, Metabolomics, Software",
  "License": "GPL-2",
  "LazyLoad": "yes",
  "Config/pak/sysreqs": "cmake libglpk-dev make libicu-dev libuv1-dev\nlibxml2-dev libnetcdf-dev libssl-dev zlib1g-dev",
  "Repository": "https://bioc-release.r-universe.dev",
  "Date/Publication": "2026-04-28 12:39:58 UTC",
  "RemoteUrl": "https://github.com/bioc/MAIT",
  "RemoteRef": "RELEASE_3_23",
  "RemoteSha": "4f43667c66614e0a4eb18b05a58c5aa0f027247d",
  "NeedsCompilation": "no",
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    "User": "root"
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    "author": "A Wokaty <andres.wokaty@sph.cuny.edu>",
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    "classes",
    "classifRatioClasses",
    "classNum",
    "featureID",
    "featureInfo",
    "featureSigID",
    "getScoresTable",
    "identifyMetabolites",
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    "plotBoxplot",
    "plotHeatmap",
    "plotPCA",
    "plotPLS",
    "plsLoadings",
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    "plsScores",
    "pvalues",
    "pvaluesCorrection",
    "rawData",
    "resultsPath",
    "sampleProcessing",
    "scores",
    "sigPeaksTable",
    "spectralSigFeatures",
    "summary",
    "Validation"
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      "name": "biotransformationsTable",
      "title": "biotransformationsTable",
      "object": "MAITtables",
      "file": "MAITtables.RData",
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      ],
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        "MASSDIFF"
      ],
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      "table": true,
      "tojson": true
    },
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      "title": "Human Metabolome Database",
      "object": "MAITtables",
      "file": "MAITtables.RData",
      "class": [
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      ],
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        "NAME",
        "FORMULA",
        "MASS",
        "Biofluid"
      ],
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      "table": true,
      "tojson": true
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    {
      "name": "MAIT",
      "title": "MAIT",
      "object": "MAIT_sample",
      "file": "MAIT_sample.RData",
      "class": [
        "MAIT"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
    {
      "name": "negAdducts",
      "title": "Negative adducts table",
      "object": "MAITtables",
      "file": "MAITtables.RData",
      "class": [
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      ],
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        "nmol",
        "charge",
        "massdiff",
        "oidscore",
        "quasi",
        "ips"
      ],
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      "table": true,
      "tojson": true
    },
    {
      "name": "posAdducts",
      "title": "Positive adducts table",
      "object": "MAITtables",
      "file": "MAITtables.RData",
      "class": [
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      ],
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        "nmol",
        "charge",
        "massdiff",
        "oidscore",
        "quasi",
        "ips"
      ],
      "rows": 26,
      "table": true,
      "tojson": true
    }
  ],
  "_help": [
    {
      "page": "Biotransformations",
      "title": "Biotransformations of the significant data contained in a MAIT object are identified.",
      "topics": [
        "Biotransformations"
      ]
    },
    {
      "page": "biotransformationsTable",
      "title": "biotransformationsTable",
      "topics": [
        "biotransformationsTable"
      ]
    },
    {
      "page": "classes",
      "title": "Class names extractor from a MAIT object",
      "topics": [
        "classes"
      ]
    },
    {
      "page": "classifRatioClasses",
      "title": "Class classification ratio extractor from a MAIT object",
      "topics": [
        "classifRatioClasses"
      ]
    },
    {
      "page": "classNum",
      "title": "Sample number extractor for each class from a MAIT object",
      "topics": [
        "classNum"
      ]
    },
    {
      "page": "Database",
      "title": "Human Metabolome Database",
      "topics": [
        "Database"
      ]
    },
    {
      "page": "featureID",
      "title": "Feature ID extractor from a MAIT object",
      "topics": [
        "featureID"
      ]
    },
    {
      "page": "featureInfo",
      "title": "Feature Info extractor from a MAIT object",
      "topics": [
        "featureInfo"
      ]
    },
    {
      "page": "featureSigID",
      "title": "Feature statistically significant ID extractor from a MAIT object",
      "topics": [
        "featureSigID"
      ]
    },
    {
      "page": "getScoresTable",
      "title": "Returns a list with the peak scores, masses, retention time and other information",
      "topics": [
        "getScoresTable"
      ]
    },
    {
      "page": "identifyMetabolites",
      "title": "Metabolite identifier",
      "topics": [
        "identifyMetabolites"
      ]
    },
    {
      "page": "loadings",
      "title": "Loadings extractor for either PCA or PLS models",
      "topics": [
        "loadings"
      ]
    },
    {
      "page": "LSDResults",
      "title": "Extractor of the Fisher's LSD tests from a MAIT object",
      "topics": [
        "LSDResults"
      ]
    },
    {
      "page": "MAIT_dataSet",
      "title": "MAIT",
      "topics": [
        "MAIT"
      ]
    },
    {
      "page": "MAIT-class",
      "title": "Class '\"MAIT\"'",
      "topics": [
        "loadings,MAIT-method",
        "MAIT-class",
        "model,MAIT-method",
        "scores,MAIT-method",
        "summary,MAIT-method"
      ]
    },
    {
      "page": "MAIT.FeatureData-class",
      "title": "Class '\"MAIT.FeatureData\"'",
      "topics": [
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      ]
    },
    {
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      "title": "Class '\"MAIT.FeatureInfo\"'",
      "topics": [
        "MAIT.FeatureInfo-class"
      ]
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    {
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      "title": "Class '\"MAIT.Parameters\"'",
      "topics": [
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      ]
    },
    {
      "page": "MAIT.PhenoData-class",
      "title": "Class '\"MAIT.PhenoData\"'",
      "topics": [
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      ]
    },
    {
      "page": "MAIT.RawData-class",
      "title": "Class '\"MAIT.RawData\"'",
      "topics": [
        "MAIT.RawData-class"
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    {
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      "title": "Class '\"MAIT.Validation\"'",
      "topics": [
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      ]
    },
    {
      "page": "MAITbuilder",
      "title": "MAIT constructor function when using external peak data",
      "topics": [
        "MAITbuilder"
      ]
    },
    {
      "page": "metaboliteTable",
      "title": "Metabolite table generator",
      "topics": [
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      "topics": [
        "model"
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    {
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      "topics": [
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    },
    {
      "page": "negAdducts",
      "title": "Negative adducts table",
      "topics": [
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      ]
    },
    {
      "page": "ovClassifRatio",
      "title": "Overall classification ratio extractor for MAIT objects",
      "topics": [
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      ]
    },
    {
      "page": "ovClassifRatioTable",
      "title": "Overall classification table extractor for MAIT objects",
      "topics": [
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    },
    {
      "page": "parameters",
      "title": "Extractor of the parameters used in the whole run from a MAIT object",
      "topics": [
        "parameters"
      ]
    },
    {
      "page": "peakAnnotation",
      "title": "Spectra constructor and peak annotator",
      "topics": [
        "peakAnnotation"
      ]
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    {
      "page": "plotBoxplot",
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      "topics": [
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      ]
    },
    {
      "page": "plotHeatmap",
      "title": "Builds ten heatmaps with different p-values and clustering distances",
      "topics": [
        "plotHeatmap"
      ]
    },
    {
      "page": "plotPCA",
      "title": "2D and 3D PCA scoreplots from a MAIT object",
      "topics": [
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      ]
    },
    {
      "page": "plotPLS",
      "title": "2D and 3D PLS scoreplots from a MAIT object",
      "topics": [
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      ]
    },
    {
      "page": "posAdducts",
      "title": "Positive adducts table",
      "topics": [
        "posAdducts"
      ]
    },
    {
      "page": "pvalues",
      "title": "Pvalues extractor from a MAIT object",
      "topics": [
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      ]
    },
    {
      "page": "pvaluesCorrection",
      "title": "P-values correction extractor from a MAIT object",
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    },
    {
      "page": "rawData",
      "title": "Raw data extractor from a MAIT object",
      "topics": [
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      ]
    },
    {
      "page": "resultsPath",
      "title": "Retrieves the folder where the results are saved for a MAIT object",
      "topics": [
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      ]
    },
    {
      "page": "sampleProcessing",
      "title": "Peak detector of netCDF samples using xcms package",
      "topics": [
        "sampleProcessing"
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    },
    {
      "page": "scores",
      "title": "Retrieves the scores from a MAIT object",
      "topics": [
        "scores"
      ]
    },
    {
      "page": "sigPeaksTable",
      "title": "Build a table of the information related to the significant features contained in a MAIT object",
      "topics": [
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    },
    {
      "page": "spectralSigFeatures",
      "title": "Extract significant features from a MAIT object",
      "topics": [
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    },
    {
      "page": "Validation",
      "title": "Cross validated classification over the output of the function 'signPeaksAnova' or function 'TStudent2Clases'",
      "topics": [
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      ]
    }
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