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  "Package": "enviGCMS",
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  "Title": "GC/LC-MS Data Analysis for Environmental Science",
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  "Authors@R": "c(person(given = \"Miao\", family = \"YU\",\nrole = c(\"aut\", \"cre\"),\nemail = \"yufreecas@gmail.com\",\ncomment = c(ORCID = \"0000-0002-2804-6014\")),\nperson(given = \"Thanh\", family = \"Wang\",\nrole = c(\"ctb\"),\nemail = \"Thanh.Wang@oru.se\",\ncomment = c(ORCID = \"0000-0002-5729-1908\")))",
  "Description": "Gas/Liquid Chromatography-Mass Spectrometer(GC/LC-MS) Data\nAnalysis for Environmental Science. This package covered topics\nsuch molecular isotope ratio, matrix effects and Short-Chain\nChlorinated Paraffins analysis etc. in environmental analysis.",
  "URL": "https://yufree.github.io/enviGCMS/",
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  "Author": "Miao YU [aut, cre] (ORCID:\n<https://orcid.org/0000-0002-2804-6014>), Thanh Wang [ctb]\n(ORCID: <https://orcid.org/0000-0002-5729-1908>)",
  "Maintainer": "Miao YU <yufreecas@gmail.com>",
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  "_exports": [
    "checkGoldenRules",
    "cleanMGF",
    "findline",
    "findlipid",
    "findmet",
    "findohc",
    "findpfc",
    "getalign",
    "getalign2",
    "getcompare",
    "getcsv",
    "getdoe",
    "getdwtus",
    "getfilter",
    "getformula",
    "getHRMF",
    "getimputation",
    "getintegration",
    "getisotopologues",
    "getmass",
    "getmassdefect",
    "getmdh",
    "getmdr",
    "getms1anno",
    "getMSP",
    "getmzrtcsv",
    "getoverlappeak",
    "getpn",
    "getpower",
    "getpqsi",
    "getrangecsv",
    "getretcor",
    "getrmd",
    "gifmr",
    "HRMF",
    "integration",
    "ma",
    "plotcc",
    "plotden",
    "plotdwtus",
    "plotEIC",
    "plotgroup",
    "plothist",
    "plothm",
    "plotint",
    "plotintslope",
    "plotkms",
    "plotmr",
    "plotmrc",
    "plotms",
    "plotmz",
    "plotpca",
    "plotpeak",
    "plotridge",
    "plotridges",
    "plotrla",
    "plotrsd",
    "plotrug",
    "plotsms",
    "plotsub",
    "plott",
    "plottic",
    "plotTopMS1Peaks",
    "plotTopMS2Peaks",
    "runMDPlot",
    "runsccp",
    "scoreIsotopes",
    "writeMSP"
  ],
  "_datasets": [
    {
      "name": "list",
      "title": "Demo data",
      "object": "list",
      "class": [
        "list"
      ],
      "fields": [],
      "table": false,
      "tojson": true
    },
    {
      "name": "matrix",
      "title": "Demo raw data matrix",
      "object": "matrix",
      "class": [
        "matrix",
        "array"
      ],
      "fields": [],
      "rows": 4001,
      "table": true,
      "tojson": true
    },
    {
      "name": "sccp",
      "title": "Short-Chain Chlorinated Paraffins(SCCPs) peaks information for quantitative analysis",
      "object": "sccp",
      "class": [
        "data.frame"
      ],
      "fields": [
        "Cln",
        "Cn",
        "formula",
        "Hn",
        "ions",
        "mz",
        "intensity",
        "Clp"
      ],
      "rows": 24,
      "table": true,
      "tojson": true
    },
    {
      "name": "TBBPA",
      "title": "Demo data for TBBPA metabolism in Pumpkin",
      "object": "TBBPA",
      "class": [
        "list"
      ],
      "fields": [],
      "table": false,
      "tojson": true
    }
  ],
  "_help": [
    {
      "page": "c.mzrt",
      "title": "c method for mzrt object",
      "topics": [
        "c.mzrt"
      ]
    },
    {
      "page": "checkGoldenRules",
      "title": "Check Chemical Formula against Fiehn Seven Golden Rules",
      "topics": [
        "checkGoldenRules"
      ]
    },
    {
      "page": "cleanMGF",
      "title": "Clean an MGF file by keeping only formula-explainable peaks",
      "topics": [
        "cleanMGF"
      ]
    },
    {
      "page": "findline",
      "title": "find line of the regression model for GC-MS",
      "topics": [
        "findline"
      ]
    },
    {
      "page": "findlipid",
      "title": "Find lipid class of metabolites base on referenced Kendrick mass defect",
      "topics": [
        "findlipid"
      ]
    },
    {
      "page": "findmet",
      "title": "Screen metabolites by Mass Defect",
      "topics": [
        "findmet"
      ]
    },
    {
      "page": "findohc",
      "title": "Screen organohalogen compounds",
      "topics": [
        "findohc"
      ]
    },
    {
      "page": "findpfc",
      "title": "Find PFCs based on mass defect analysis",
      "topics": [
        "findpfc"
      ]
    },
    {
      "page": "getalign",
      "title": "Align two peaks vectors by mass to charge ratio and/or retention time",
      "topics": [
        "getalign"
      ]
    },
    {
      "page": "getalign2",
      "title": "Align mass to charge ratio and/or retention time to remove redundancy",
      "topics": [
        "getalign2"
      ]
    },
    {
      "page": "getcompare",
      "title": "Align multiple peaks list to one peak list",
      "topics": [
        "getcompare"
      ]
    },
    {
      "page": "getcsv",
      "title": "Convert an list object to csv file",
      "topics": [
        "getcsv"
      ]
    },
    {
      "page": "getdoe",
      "title": "Generate the group level rsd and average intensity based on DoE,",
      "topics": [
        "getdoe"
      ]
    },
    {
      "page": "getdwtus",
      "title": "Density weighted intensity for one sample",
      "topics": [
        "getdwtus"
      ]
    },
    {
      "page": "getfilter",
      "title": "Filter the data based on row and column index",
      "topics": [
        "getfilter"
      ]
    },
    {
      "page": "getformula",
      "title": "Get chemical formula for mass to charge ratio using the HORIZON algorithm",
      "topics": [
        "getformula"
      ]
    },
    {
      "page": "getHRMF",
      "title": "Batch High Resolution Mass Filtering for all compounds in an MSP file",
      "topics": [
        "getHRMF"
      ]
    },
    {
      "page": "getimputation",
      "title": "Impute the peaks list data",
      "topics": [
        "getimputation"
      ]
    },
    {
      "page": "getintegration",
      "title": "getintegration was mainly used for get the integration of certain ion's chromatogram data and plot the data",
      "topics": [
        "getintegration"
      ]
    },
    {
      "page": "getisotopologues",
      "title": "Get the selected isotopologues at certain MS data",
      "topics": [
        "getisotopologues"
      ]
    },
    {
      "page": "getmass",
      "title": "Get the exact mass of the isotopologues from a chemical formula or reaction's isotope patterns with the highest abundances",
      "topics": [
        "getmass"
      ]
    },
    {
      "page": "getmassdefect",
      "title": "Get mass defect with certain scaled factor",
      "topics": [
        "getmassdefect"
      ]
    },
    {
      "page": "getmdh",
      "title": "Get the high order unit based Mass Defect",
      "topics": [
        "getmdh"
      ]
    },
    {
      "page": "getmdr",
      "title": "Get the raw Mass Defect",
      "topics": [
        "getmdr"
      ]
    },
    {
      "page": "getms1anno",
      "title": "Annotation of MS1 data by compounds database by predefined paired mass distance",
      "topics": [
        "getms1anno"
      ]
    },
    {
      "page": "getMSP",
      "title": "read in MSP file as list for ms/ms or ms(EI) annotation",
      "topics": [
        "getMSP"
      ]
    },
    {
      "page": "getmzrtcsv",
      "title": "Covert the peaks list csv file into list",
      "topics": [
        "getmzrtcsv"
      ]
    },
    {
      "page": "getoverlappeak",
      "title": "Get the overlap peaks by mass and retention time range",
      "topics": [
        "getoverlappeak"
      ]
    },
    {
      "page": "getpn",
      "title": "Merge positive and negative mode data",
      "topics": [
        "getpn"
      ]
    },
    {
      "page": "getpower",
      "title": "Get the index with power restriction for certain study with BH adjusted p-value and certain power",
      "topics": [
        "getpower"
      ]
    },
    {
      "page": "getpqsi",
      "title": "Compute pooled QC linear index according to run order",
      "topics": [
        "getpqsi"
      ]
    },
    {
      "page": "getrangecsv",
      "title": "Get a mzrt list and/or save mz and rt range as csv file",
      "topics": [
        "getrangecsv"
      ]
    },
    {
      "page": "getretcor",
      "title": "Perform peaks list alignment and return features table",
      "topics": [
        "getretcor"
      ]
    },
    {
      "page": "getrmd",
      "title": "Get the Relative Mass Defect",
      "topics": [
        "getrmd"
      ]
    },
    {
      "page": "gifmr",
      "title": "plot scatter plot for rt-mz profile and output gif file for multiple groups",
      "topics": [
        "gifmr"
      ]
    },
    {
      "page": "HRMF",
      "title": "High Resolution Mass Filtering (HRMF) for GC/LC HRMS data",
      "topics": [
        "HRMF"
      ]
    },
    {
      "page": "integration",
      "title": "Just integrate data according to fixed rt and fixed noise area",
      "topics": [
        "integration"
      ]
    },
    {
      "page": "list",
      "title": "Demo data",
      "topics": [
        "list"
      ]
    },
    {
      "page": "ma",
      "title": "filter data by average moving box",
      "topics": [
        "ma"
      ]
    },
    {
      "page": "matrix",
      "title": "Demo raw data matrix",
      "topics": [
        "matrix"
      ]
    },
    {
      "page": "plotcc",
      "title": "Plot the calibration curve with error bar, r squared and equation",
      "topics": [
        "plotcc"
      ]
    },
    {
      "page": "plotden",
      "title": "plot the density for multiple samples",
      "topics": [
        "plotden"
      ]
    },
    {
      "page": "plotdwtus",
      "title": "plot density weighted intensity for multiple samples",
      "topics": [
        "plotdwtus"
      ]
    },
    {
      "page": "plotEIC",
      "title": "Plot extracted ion chromatograms from raw mzML/mzXML data",
      "topics": [
        "plotEIC"
      ]
    },
    {
      "page": "plotgroup",
      "title": "Plot the response group of GC-MS",
      "topics": [
        "plotgroup"
      ]
    },
    {
      "page": "plothist",
      "title": "Plot the density of the GC-MS data with EM algorithm to separate the data into two log normal distribution",
      "topics": [
        "plothist"
      ]
    },
    {
      "page": "plothm",
      "title": "Plot the heatmap of mzrt profiles",
      "topics": [
        "plothm"
      ]
    },
    {
      "page": "plotint",
      "title": "plot the information of integration",
      "topics": [
        "plotint"
      ]
    },
    {
      "page": "plotintslope",
      "title": "plot the slope information of integration",
      "topics": [
        "plotintslope"
      ]
    },
    {
      "page": "plotkms",
      "title": "plot the kendrick mass defect diagram",
      "topics": [
        "plotkms"
      ]
    },
    {
      "page": "plotmr",
      "title": "plot the scatter plot for peaks list with threshold",
      "topics": [
        "plotmr"
      ]
    },
    {
      "page": "plotmrc",
      "title": "plot the diff scatter plot for peaks list with threshold between two groups",
      "topics": [
        "plotmrc"
      ]
    },
    {
      "page": "plotms",
      "title": "plot GC/LC-MS data as a heatmap with TIC",
      "topics": [
        "plotms"
      ]
    },
    {
      "page": "plotmz",
      "title": "plot GC/LC-MS data as scatter plot",
      "topics": [
        "plotmz"
      ]
    },
    {
      "page": "plotpca",
      "title": "plot the PCA for multiple samples",
      "topics": [
        "plotpca"
      ]
    },
    {
      "page": "plotpeak",
      "title": "plot intensity of peaks across samples or samples across peaks",
      "topics": [
        "plotpeak"
      ]
    },
    {
      "page": "plotridge",
      "title": "plot ridgeline density plot",
      "topics": [
        "plotridge"
      ]
    },
    {
      "page": "plotridges",
      "title": "Relative Log Abundance Ridge (RLAR) plots for samples or peaks",
      "topics": [
        "plotridges"
      ]
    },
    {
      "page": "plotrla",
      "title": "Relative Log Abundance (RLA) plots",
      "topics": [
        "plotrla"
      ]
    },
    {
      "page": "plotrsd",
      "title": "plot the rsd influences of data in different groups",
      "topics": [
        "plotrsd"
      ]
    },
    {
      "page": "plotrug",
      "title": "plot 1-d density for multiple samples",
      "topics": [
        "plotrug"
      ]
    },
    {
      "page": "plotsms",
      "title": "Plot the intensity distribution of GC-MS",
      "topics": [
        "plotsms"
      ]
    },
    {
      "page": "plotsub",
      "title": "Plot the background of data",
      "topics": [
        "plotsub"
      ]
    },
    {
      "page": "plott",
      "title": "plot GC-MS data as a heatmap for constant speed of temperature rising",
      "topics": [
        "plott"
      ]
    },
    {
      "page": "plottic",
      "title": "Plot Total Ion Chromatogram (TIC)",
      "topics": [
        "plottic"
      ]
    },
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      "page": "plotTopMS1Peaks",
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