{
  "_id": "6a1aef821d7bb097a09f6316",
  "Package": "ptairMS",
  "Title": "Pre-processing PTR-TOF-MS Data",
  "Version": "1.21.0",
  "Date": "2020-03-18",
  "Authors@R": "person(\"camille\", \"Roquencourt\", email = \"camille.roquencourt@hotmail.fr\", role = c(\"aut\", \"cre\"))",
  "Description": "This package implements a suite of methods to preprocess\ndata from PTR-TOF-MS instruments (HDF5 format) and generates\nthe 'sample by features' table of peak intensities in addition\nto the sample and feature metadata (as a singl<e ExpressionSet\nobject for subsequent statistical analysis). This package also\npermit usefull tools for cohorts management as analyzing data\nprogressively, visualization tools and quality control. The\nsteps include calibration, expiration detection, peak detection\nand quantification, feature alignment, missing value imputation\nand feature annotation. Applications to exhaled air and cell\nculture in headspace are described in the vignettes and\nexamples. This package was used for data analysis of Gassin\nDelyle study on adults undergoing invasive mechanical\nventilation in the intensive care unit due to severe COVID-19\nor non-COVID-19 acute respiratory distress syndrome (ARDS), and\npermit to identfy four potentiel biomarquers of the infection.",
  "License": "GPL-3",
  "Encoding": "UTF-8",
  "BugReports": "https://github.com/camilleroquencourt/ptairMS/issues",
  "RoxygenNote": "7.2.3",
  "VignetteBuilder": "knitr",
  "NeedsCompilation": "yes",
  "biocViews": "Software, MassSpectrometry, Preprocessing, Metabolomics,\nPeakDetection, Alignment",
  "Config/pak/sysreqs": "cmake libglpk-dev make libicu-dev libuv1-dev\nlibxml2-dev libnetcdf-dev libssl-dev zlib1g-dev",
  "Repository": "https://bioc.r-universe.dev",
  "Date/Publication": "2026-04-28 12:55:37 UTC",
  "RemoteUrl": "https://github.com/bioc/ptairMS",
  "RemoteRef": "HEAD",
  "RemoteSha": "258decba3c9deb98696635441ba25eb7a6b8b051",
  "Packaged": {
    "Date": "2026-05-30 09:41:52 UTC",
    "User": "root"
  },
  "Author": "camille Roquencourt [aut, cre]",
  "Maintainer": "camille Roquencourt <camille.roquencourt@hotmail.fr>",
  "MD5sum": "3897af8f5466363a160cfd8ce9d27d3a",
  "_user": "bioc",
  "_type": "src",
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  "_created": "2026-05-30T09:41:52.000Z",
  "_published": "2026-05-30T14:09:06.254Z",
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  "_buildurl": "https://github.com/r-universe/bioc/actions/runs/26676210194",
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  "_host": "GitHub-Actions",
  "_upstream": "https://github.com/bioc/ptairMS",
  "_commit": {
    "id": "258decba3c9deb98696635441ba25eb7a6b8b051",
    "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": 1777380937
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    "massspectrometry",
    "preprocessing",
    "metabolomics",
    "peakdetection",
    "alignment",
    "cpp"
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    "source": "https://www.bioconductor.org/packages/stats/bioc/ptairMS"
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  "_rbuild": "4.6.0",
  "_assets": [
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    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/contents.json",
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    "extra/NEWS.txt",
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  "_homeurl": "https://github.com/camilleroquencourt/ptairms",
  "_realowner": "bioc",
  "_cranurl": false,
  "_exports": [
    "alignSamples",
    "annotateVOC",
    "calibration",
    "changeTimeLimits",
    "convert_to_mzML",
    "createPtrSet",
    "defineKnots",
    "detectPeak",
    "exportSampleMetada",
    "formula2mass",
    "getDirectory",
    "getFileNames",
    "getPeakList",
    "getSampleMetadata",
    "importSampleMetadata",
    "impute",
    "imputeMat",
    "LocalMaximaSG",
    "PeakList",
    "plot",
    "plotCalib",
    "plotFeatures",
    "plotRaw",
    "plotTIC",
    "readRaw",
    "resetSampleMetadata",
    "rmPeakList",
    "RunShinnyApp",
    "setSampleMetadata",
    "show",
    "timeLimits",
    "updatePtrSet",
    "writeEset"
  ],
  "_help": [
    {
      "page": "aggregate",
      "title": "aggregate peakgroup for align function",
      "topics": [
        "aggregate"
      ]
    },
    {
      "page": "alignSamples",
      "title": "Alignment between samples",
      "topics": [
        "alignSamples",
        "alignSamples,ptrSet-method"
      ]
    },
    {
      "page": "annotation",
      "title": "Putative annotation of VOC mz by using the reference compilation from the literature",
      "topics": [
        "annotateVOC",
        "annotateVOC,data.frame-method",
        "annotateVOC,ExpressionSet-method",
        "annotateVOC,numeric-method"
      ]
    },
    {
      "page": "calibration",
      "title": "Calibrates the mass axis with references masses",
      "topics": [
        "calibration",
        "calibration,ptrRaw-method",
        "calibration,ptrSet-method"
      ]
    },
    {
      "page": "changeTimeLimits",
      "title": "Shinny appplication to modify and view expiration limits This function run a shiny app, where you can check the automatic expiration detection, knots location, and modify it.",
      "topics": [
        "changeTimeLimits"
      ]
    },
    {
      "page": "convert_to_mzML",
      "title": "Convert a h5 file to mzML",
      "topics": [
        "convert_to_mzML"
      ]
    },
    {
      "page": "createPtrSet",
      "title": "Creates a ptrSet object form a directory",
      "topics": [
        "createPtrSet"
      ]
    },
    {
      "page": "defineKnots",
      "title": "Define the knots location",
      "topics": [
        "defineKnots",
        "defineKnots,ptrRaw-method",
        "defineKnots,ptrSet-method"
      ]
    },
    {
      "page": "detectPeak",
      "title": "Detection and quantification of peaks for a ptrSet object.",
      "topics": [
        "detectPeak",
        "detectPeak,ptrRaw-method",
        "detectPeak,ptrSet-method"
      ]
    },
    {
      "page": "exportSampleMetada",
      "title": "export sampleMetadata",
      "topics": [
        "exportSampleMetada"
      ]
    },
    {
      "page": "formula2mass",
      "title": "Compute exact mass.",
      "topics": [
        "formula2mass"
      ]
    },
    {
      "page": "getDirectory",
      "title": "get the files directory of a ptrSet",
      "topics": [
        "getDirectory"
      ]
    },
    {
      "page": "getFileNames",
      "title": "get the file names containing in the directory of a ptrSet or ptrRaw",
      "topics": [
        "getFileNames",
        "getFileNames,ptrRaw-method",
        "getFileNames,ptrSet-method"
      ]
    },
    {
      "page": "getPeakList",
      "title": "get the peak list of a ptrSet object",
      "topics": [
        "getPeakList"
      ]
    },
    {
      "page": "getSampleMetadata",
      "title": "get sampleMetadata of a ptrSet",
      "topics": [
        "getSampleMetadata"
      ]
    },
    {
      "page": "importSampleMetadata",
      "title": "import a sampleMetadata from a tsv file to a ptrSet object",
      "topics": [
        "importSampleMetadata"
      ]
    },
    {
      "page": "impute",
      "title": "Imputes the missing values",
      "topics": [
        "impute"
      ]
    },
    {
      "page": "imputeMat",
      "title": "Impute missing values on an matrix set from an ptrSet",
      "topics": [
        "imputeMat"
      ]
    },
    {
      "page": "LocalMaximaSG",
      "title": "Find local maxima with Savitzky Golay filter",
      "topics": [
        "LocalMaximaSG"
      ]
    },
    {
      "page": "PeakList",
      "title": "Detection and quantification of peaks on a sum spectrum.",
      "topics": [
        "PeakList",
        "PeakList,ptrRaw-method"
      ]
    },
    {
      "page": "plot",
      "title": "Plot a ptrSet object",
      "topics": [
        "plot,ptrSet,ANY-method",
        "plot,ptrSet-method",
        "plot.ptrSet"
      ]
    },
    {
      "page": "plotCalib",
      "title": "Plot the calibration peaks after calibration",
      "topics": [
        "plotCalib",
        "plotCalib,ptrRaw-method",
        "plotCalib,ptrSet-method"
      ]
    },
    {
      "page": "plotFeatures",
      "title": "Plot raw average spectrum around a mzRange",
      "topics": [
        "plotFeatures",
        "plotFeatures,ptrSet-method"
      ]
    },
    {
      "page": "plotRaw",
      "title": "Plot method for 'ptrRaw' objects",
      "topics": [
        "plotRaw",
        "plotRaw,ptrRaw-method",
        "plotRaw,ptrSet-method"
      ]
    },
    {
      "page": "plotTIC",
      "title": "plot the Total Ion sptectrum (TIC) for one or several files.",
      "topics": [
        "plotTIC",
        "plotTIC,ptrRaw-method",
        "plotTIC,ptrSet-method"
      ]
    },
    {
      "page": "ptrRaw",
      "title": "PTR-TOF-MS raw data from a rhdf5 file",
      "topics": [
        "ptrRaw-class"
      ]
    },
    {
      "page": "ptrSet",
      "title": "A set of PTR-TOF-MS raw data informations",
      "topics": [
        "ptrSet-class"
      ]
    },
    {
      "page": "readRaw",
      "title": "Read a h5 file of PTR-TOF-MS data",
      "topics": [
        "readRaw"
      ]
    },
    {
      "page": "resetSampleMetadata",
      "title": "reset the default sampleMetadata, containing the suborders names and the acquisition dates as columns.",
      "topics": [
        "resetSampleMetadata"
      ]
    },
    {
      "page": "rmPeakList",
      "title": "remove the peakList of an ptrSet object",
      "topics": [
        "rmPeakList"
      ]
    },
    {
      "page": "RunShinnyApp",
      "title": "Graphical interface of ptairMS workflow",
      "topics": [
        "RunShinnyApp"
      ]
    },
    {
      "page": "setSampleMetadata",
      "title": "set sampleMetadata in a ptrSet",
      "topics": [
        "setSampleMetadata"
      ]
    },
    {
      "page": "show-ptrRaw-method",
      "title": "show a ptrRaw object",
      "topics": [
        "show,ptrRaw-method"
      ]
    },
    {
      "page": "show-ptrSet-method",
      "title": "show a ptrSet object",
      "topics": [
        "show,ptrSet-method"
      ]
    },
    {
      "page": "timeLimits",
      "title": "Calculates time limits on the breath tracer",
      "topics": [
        "timeLimits",
        "timeLimits,ptrRaw-method",
        "timeLimits,ptrSet-method"
      ]
    },
    {
      "page": "updatePtrSet",
      "title": "update a ptrSet object",
      "topics": [
        "updatePtrSet"
      ]
    },
    {
      "page": "writeEset",
      "title": "Exporting an ExpressionSet instance into 3 tabulated files 'dataMatrix.tsv', sampleMetadata.tsv', and 'variableMetadata.tsv'",
      "topics": [
        "writeEset",
        "writeEset,ExpressionSet-method"
      ]
    }
  ],
  "_readme": "https://github.com/bioc/ptairMS/raw/HEAD/README.md",
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        "Datasets (ptairData package)",
        "Hands on",
        "Graphical Interface",
        "createPtrSet: Checking raw data and setting parameters",
        "Calibrating the mass axis",
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