{
  "_id": "6a1ee228b401979e73410b2d",
  "Package": "MALDIquant",
  "Version": "1.22.3",
  "Date": "2024-08-19",
  "Title": "Quantitative Analysis of Mass Spectrometry Data",
  "Authors@R": "c(\nperson(\ngiven = \"Sebastian\", family = \"Gibb\",\nemail=\"mail@sebastiangibb.de\",\ncomment=c(ORCID=\"0000-0001-7406-4443\"),\nrole = c(\"aut\", \"cre\")\n),\nperson(\ngiven = \"Korbinian\", family = \"Strimmer\",\ncomment=c(ORCID=\"0000-0001-7917-2056\"),\nrole=\"ths\"\n),\nperson(given = \"Sigurdur\", family = \"Smarason\", role = \"ctb\"),\nperson(\ngiven = \"Laurent\", family = \"Gatto\",\nemail = \"laurent.gatto@uclouvain.be\",\ncomment = c(ORCID = \"0000-0002-1520-2268\"),\nrole = \"ctb\"\n),\nperson(given = \"Paolo\", family = \"Inglese\", role = \"ctb\"))",
  "Description": "A complete analysis pipeline for matrix-assisted laser\ndesorption/ionization-time-of-flight (MALDI-TOF) and other\ntwo-dimensional mass spectrometry data. In addition to commonly\nused plotting and processing methods it includes distinctive\nfeatures, namely baseline subtraction methods such as\nmorphological filters (TopHat) or the statistics-sensitive\nnon-linear iterative peak-clipping algorithm (SNIP), peak\nalignment using warping functions, handling of replicated\nmeasurements as well as allowing spectra with different\nresolutions.",
  "License": "GPL (>= 3)",
  "URL": "https://strimmerlab.github.io/software/maldiquant/,\nhttps://github.com/sgibb/MALDIquant/",
  "BugReports": "https://github.com/sgibb/MALDIquant/issues/",
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    "User": "root"
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  "Author": "Sebastian Gibb [aut, cre]\n(<https://orcid.org/0000-0001-7406-4443>), Korbinian Strimmer\n[ths] (<https://orcid.org/0000-0001-7917-2056>), Sigurdur\nSmarason [ctb], Laurent Gatto [ctb]\n(<https://orcid.org/0000-0002-1520-2268>), Paolo Inglese [ctb]",
  "Maintainer": "Sebastian Gibb <mail@sebastiangibb.de>",
  "Repository": "https://sgibb.r-universe.dev",
  "Date/Publication": "2024-08-20 02:48:33 UTC",
  "RemoteUrl": "https://github.com/cran/MALDIquant",
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  "_published": "2026-06-02T14:01:12.815Z",
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    "extra/citation.json",
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    "manual.pdf"
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  "_exports": [
    "alignSpectra",
    "as.matrix",
    "averageMassSpectra",
    "binPeaks",
    "calibrateIntensity",
    "coordinates",
    "coordinates<-",
    "createMassPeaks",
    "createMassSpectrum",
    "detectPeaks",
    "determineWarpingFunctions",
    "estimateBaseline",
    "estimateNoise",
    "filterPeaks",
    "findEmptyMassObjects",
    "intensity",
    "intensity<-",
    "intensityMatrix",
    "isEmpty",
    "isMassPeaks",
    "isMassPeaksList",
    "isMassSpectrum",
    "isMassSpectrumList",
    "isRegular",
    "labelPeaks",
    "lines",
    "mass",
    "mass<-",
    "match.closest",
    "mergeMassPeaks",
    "metaData",
    "metaData<-",
    "monoisotopicPeaks",
    "msiSlices",
    "mz",
    "mz<-",
    "plot",
    "plotMsiSlice",
    "points",
    "referencePeaks",
    "removeBaseline",
    "removeEmptyMassObjects",
    "smoothIntensity",
    "snr",
    "totalIonCurrent",
    "transformIntensity",
    "trim",
    "warpMassPeaks",
    "warpMassSpectra"
  ],
  "_datasets": [
    {
      "name": "fiedler2009subset",
      "title": "Example Mass Spectra (raw)",
      "object": "fiedler2009subset",
      "file": "fiedler2009subset.RData",
      "class": [
        "list"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    }
  ],
  "_help": [
    {
      "page": "MALDIquant-package",
      "title": "Quantitative Analysis of Mass Spectrometry Data",
      "topics": [
        "MALDIquant-package",
        "MALDIquant"
      ]
    },
    {
      "page": "AbstractMassObject-class",
      "title": "Class \"AbstractMassObject\"",
      "topics": [
        "AbstractMassObject-class",
        "as.matrix,AbstractMassObject-method",
        "coordinates",
        "coordinates,AbstractMassObject-method",
        "coordinates,list-method",
        "coordinates<-",
        "coordinates<-,AbstractMassObject,matrix-method",
        "coordinates<-,AbstractMassObject,numeric-method",
        "coordinates<-,list,matrix-method",
        "intensity",
        "intensity,AbstractMassObject-method",
        "intensity<-",
        "intensity<-,AbstractMassObject,numeric-method",
        "isEmpty",
        "isEmpty,AbstractMassObject-method",
        "length,AbstractMassObject-method",
        "lines,AbstractMassObject-method",
        "mass",
        "mass,AbstractMassObject-method",
        "mass<-",
        "mass<-,AbstractMassObject,numeric-method",
        "metaData",
        "metaData,AbstractMassObject-method",
        "metaData<-",
        "metaData<-,AbstractMassObject-method",
        "mz",
        "mz,AbstractMassObject-method",
        "mz<-",
        "mz<-,AbstractMassObject,numeric-method",
        "points,AbstractMassObject-method",
        "[,AbstractMassObject,logical,missing-method",
        "[,AbstractMassObject,numeric,missing-method",
        "[,MassPeaks,logical,missing-method",
        "[,MassPeaks,numeric,missing-method"
      ]
    },
    {
      "page": "alignSpectra-functions",
      "title": "Align MassSpectrum objects.",
      "topics": [
        "alignSpectra"
      ]
    },
    {
      "page": "averageMassSpectra-functions",
      "title": "Averages 'MassSpectrum' objects.",
      "topics": [
        "averageMassSpectra"
      ]
    },
    {
      "page": "binPeaks-functions",
      "title": "Align Peaks into discrete bins.",
      "topics": [
        "binPeaks"
      ]
    },
    {
      "page": "calibrateIntensity-methods",
      "title": "Calibrates intensities of a MassSpectrum object.",
      "topics": [
        "calibrateIntensity",
        "calibrateIntensity,list-method",
        "calibrateIntensity,MassSpectrum-method"
      ]
    },
    {
      "page": "createMassPeaks-functions",
      "title": "Creates a MassPeaks object.",
      "topics": [
        "createMassPeaks"
      ]
    },
    {
      "page": "createMassSpectrum-functions",
      "title": "Creates a MassSpectrum object.",
      "topics": [
        "createMassSpectrum"
      ]
    },
    {
      "page": "detectPeaks-methods",
      "title": "Detects peaks in a MassSpectrum object.",
      "topics": [
        "detectPeaks",
        "detectPeaks,list-method",
        "detectPeaks,MassSpectrum-method"
      ]
    },
    {
      "page": "determineWarpingFunctions-functions",
      "title": "Determine warping functions of MassPeaks objects.",
      "topics": [
        "determineWarpingFunctions"
      ]
    },
    {
      "page": "estimateBaseline-methods",
      "title": "Estimates the baseline of a MassSpectrum object.",
      "topics": [
        "estimateBaseline",
        "estimateBaseline,MassSpectrum-method"
      ]
    },
    {
      "page": "estimateNoise-methods",
      "title": "Estimates the noise of a MassSpectrum object.",
      "topics": [
        "estimateNoise",
        "estimateNoise,MassSpectrum-method"
      ]
    },
    {
      "page": "fiedler2009subset",
      "title": "Example Mass Spectra (raw)",
      "topics": [
        "fiedler2009subset"
      ]
    },
    {
      "page": "filterPeaks-functions",
      "title": "Removes less frequent peaks.",
      "topics": [
        "filterPeaks"
      ]
    },
    {
      "page": "findEmptyMassObjects-functions",
      "title": "Finds or removes empty AbstractMassObject objects in a list.",
      "topics": [
        "findEmptyMassObjects",
        "removeEmptyMassObjects"
      ]
    },
    {
      "page": "intensityMatrix-functions",
      "title": "Converts a list of MassPeaks objects into a matrix.",
      "topics": [
        "intensityMatrix"
      ]
    },
    {
      "page": "isMassObject-functions",
      "title": "Tests for MassSpectrum or MassPeaks object.",
      "topics": [
        "isMassPeaks",
        "isMassSpectrum"
      ]
    },
    {
      "page": "isMassObjectList-functions",
      "title": "Tests a list of MassSpectrum or MassPeaks objects.",
      "topics": [
        "isMassPeaksList",
        "isMassSpectrumList"
      ]
    },
    {
      "page": "labelPeaks-methods",
      "title": "Draws peak labels to plot.",
      "topics": [
        "labelPeaks",
        "labelPeaks,MassPeaks-method"
      ]
    },
    {
      "page": "MALDIquant-parallel",
      "title": "Parallel Support in Package 'MALDIquant'",
      "topics": [
        "MALDIquant-parallel"
      ]
    },
    {
      "page": "MassPeaks-class",
      "title": "Class \"MassPeaks\"",
      "topics": [
        "MassPeaks",
        "MassPeaks-class",
        "snr",
        "snr,MassPeaks-method"
      ]
    },
    {
      "page": "MassSpectrum-class",
      "title": "Class \"MassSpectrum\"",
      "topics": [
        "isRegular",
        "isRegular,MassSpectrum-method",
        "MassSpectrum",
        "MassSpectrum-class",
        "totalIonCurrent",
        "totalIonCurrent,MassSpectrum-method"
      ]
    },
    {
      "page": "match.closest",
      "title": "Relaxed Value Matching",
      "topics": [
        "match.closest"
      ]
    },
    {
      "page": "mergeMassPeaks-functions",
      "title": "Merges 'MassPeaks' objects.",
      "topics": [
        "mergeMassPeaks"
      ]
    },
    {
      "page": "monoisotopicPeaks-methods",
      "title": "Finds monoisotopic peaks in a MassPeaks object.",
      "topics": [
        "monoisotopicPeaks",
        "monoisotopicPeaks,list-method",
        "monoisotopicPeaks,MassPeaks-method"
      ]
    },
    {
      "page": "msiSlices-functions",
      "title": "Turn a list of AbstractMassObjects into a mass spectrometry imaging slice.",
      "topics": [
        "msiSlices"
      ]
    },
    {
      "page": "plot-methods",
      "title": "Plots an AbstractMassObject object.",
      "topics": [
        "plot,AbstractMassObject,missing-method",
        "plot,MassSpectrum,missing-method"
      ]
    },
    {
      "page": "plotMsiSlice-methods",
      "title": "Plots a Mass Spectrometry Imaging dataset.",
      "topics": [
        "plotMsiSlice",
        "plotMsiSlice,array-method",
        "plotMsiSlice,list-method",
        "plotMsiSlice,matrix-method"
      ]
    },
    {
      "page": "referencePeaks-functions",
      "title": "Creates a reference 'MassPeaks' object.",
      "topics": [
        "referencePeaks"
      ]
    },
    {
      "page": "removeBaseline-methods",
      "title": "Removes the baseline of a MassSpectrum object.",
      "topics": [
        "removeBaseline",
        "removeBaseline,list-method",
        "removeBaseline,MassSpectrum-method"
      ]
    },
    {
      "page": "smoothIntensity-methods",
      "title": "Smoothes intensities of a MassSpectrum object.",
      "topics": [
        "smoothIntensity",
        "smoothIntensity,list-method",
        "smoothIntensity,MassSpectrum-method"
      ]
    },
    {
      "page": "transformIntensity-methods",
      "title": "Transforms intensities of an AbstractMassObject object.",
      "topics": [
        "transformIntensity",
        "transformIntensity,AbstractMassObject-method",
        "transformIntensity,list-method"
      ]
    },
    {
      "page": "trim-methods",
      "title": "Trim an AbstractMassObject object.",
      "topics": [
        "trim",
        "trim,AbstractMassObject,numeric-method",
        "trim,list,missing-method",
        "trim,list,numeric-method"
      ]
    },
    {
      "page": "warp-functions",
      "title": "Run warping functions on AbstractMassObject objects.",
      "topics": [
        "warpMassPeaks",
        "warpMassSpectra"
      ]
    }
  ],
  "_rundeps": [],
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      "source": "MALDIquant-intro.Rnw",
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