{
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  "Package": "RaMS",
  "Type": "Package",
  "Title": "R Access to Mass-Spec Data",
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  "Authors@R": "c(\nperson(given = \"William\", family = \"Kumler\", email = \"wkumler@uw.edu\",\nrole = c(\"aut\", \"cre\", \"cph\")),\nperson(given = \"Ricardo\", family = \"Cunha\", role = \"ctb\"),\nperson(given = \"Ethan\", family = \"Bass\", role = \"ctb\")\n)",
  "Maintainer": "William Kumler <wkumler@uw.edu>",
  "Description": "R-based access to mass-spectrometry (MS) data. While many\npackages exist to process MS data, many of these make it\ndifficult to access the underlying mass-to-charge ratio (m/z),\nintensity, and retention time of the files themselves. This\npackage is designed to format MS data in a tidy fashion and\nallows the user perform the plotting and analysis.",
  "License": "MIT + file LICENSE",
  "URL": "https://github.com/wkumler/RaMS",
  "BugReports": "https://github.com/wkumler/RaMS/issues",
  "Encoding": "UTF-8",
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  "VignetteBuilder": "knitr",
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  "Repository": "https://wkumler.r-universe.dev",
  "Date/Publication": "2026-10-07 15:28:09 UTC",
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  "RemoteRef": "HEAD",
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  "NeedsCompilation": "no",
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    "User": "root"
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  "Author": "William Kumler [aut, cre, cph],\nRicardo Cunha [ctb],\nEthan Bass [ctb]",
  "_user": "wkumler",
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  "_created": "2026-10-07T17:54:55.000Z",
  "_published": "2026-10-07T17:59:48.647Z",
  "_buildurl": "https://github.com/r-universe/wkumler/actions/runs/37662159270",
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  "_usedby": 8,
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      "week": "2026-41",
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  "_topics": [
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    "tidy-data"
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  "_realowner": "wkumler",
  "_cranurl": true,
  "_releases": [
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      "date": "2021-03-22"
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    },
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    "%inrange%",
    "editMSfileRTs",
    "grabAccessionData",
    "grabMSdata",
    "grabMzmlData",
    "grabMzxmlData",
    "minifyMSdata",
    "msdata_connection",
    "mz_group",
    "pmppm",
    "pmppm_vec",
    "qplotMS1data",
    "qplotMS2data",
    "tmzmlMaker",
    "trapz"
  ],
  "_help": [
    {
      "page": "sub-.msdata_connection",
      "title": "S3 indexing for msdata_connection objects",
      "topics": [
        "[.msdata_connection"
      ]
    },
    {
      "page": "cash-.msdata_connection",
      "title": "S3 dollar sign notation for msdata_connection objects",
      "topics": [
        "$.msdata_connection"
      ]
    },
    {
      "page": "checkOutputQuality",
      "title": "Check that the output data is properly formatted.",
      "topics": [
        "checkOutputQuality"
      ]
    },
    {
      "page": "editMSfileRTs",
      "title": "Edit mzML/mzXML file retention times",
      "topics": [
        "editMSfileRTs"
      ]
    },
    {
      "page": "getEncoded",
      "title": "Convert from compressed binary to R numeric vector",
      "topics": [
        "getEncoded"
      ]
    },
    {
      "page": "giveEncoding",
      "title": "Convert from R numeric vector to compressed binary",
      "topics": [
        "giveEncoding"
      ]
    },
    {
      "page": "grabAccessionData",
      "title": "Get arbitrary metadata from an mzML file by accession number",
      "topics": [
        "grabAccessionData"
      ]
    },
    {
      "page": "grabMSdata",
      "title": "Grab mass-spectrometry data from file(s)",
      "topics": [
        "grabMSdata"
      ]
    },
    {
      "page": "grabMzmlBPC",
      "title": "Grab the BPC or TIC from a file",
      "topics": [
        "grabMzmlBPC"
      ]
    },
    {
      "page": "grabMzmlDAD",
      "title": "Extract the DAD data from an mzML nodeset",
      "topics": [
        "grabMzmlDAD"
      ]
    },
    {
      "page": "grabMzmlData",
      "title": "Get mass-spectrometry data from an mzML file",
      "topics": [
        "grabMzmlData"
      ]
    },
    {
      "page": "grabMzmlEncodingData",
      "title": "Helper function to extract mzML file encoding data",
      "topics": [
        "grabMzmlEncodingData"
      ]
    },
    {
      "page": "grabMzmlMetadata",
      "title": "Helper function to extract mzML file metadata",
      "topics": [
        "grabMzmlMetadata"
      ]
    },
    {
      "page": "grabMzmlMS1",
      "title": "Extract the MS1 data from an mzML nodeset",
      "topics": [
        "grabMzmlMS1"
      ]
    },
    {
      "page": "grabMzmlMS2",
      "title": "Extract the MS2 data from an mzML nodeset",
      "topics": [
        "grabMzmlMS2"
      ]
    },
    {
      "page": "grabMzmlMS3",
      "title": "Extract the MS3 data from an mzML nodeset",
      "topics": [
        "grabMzmlMS3"
      ]
    },
    {
      "page": "grabMzxmlBPC",
      "title": "Grab the BPC or TIC from a file",
      "topics": [
        "grabMzxmlBPC"
      ]
    },
    {
      "page": "grabMzxmlData",
      "title": "Get mass-spectrometry data from an mzXML file",
      "topics": [
        "grabMzxmlData"
      ]
    },
    {
      "page": "grabMzxmlEncodingData",
      "title": "Helper function to extract mzXML file metadata",
      "topics": [
        "grabMzxmlEncodingData"
      ]
    },
    {
      "page": "grabMzxmlMetadata",
      "title": "Helper function to extract mzXML file metadata",
      "topics": [
        "grabMzxmlMetadata"
      ]
    },
    {
      "page": "grabMzxmlMS1",
      "title": "Extract the MS1 data from an mzXML nodeset",
      "topics": [
        "grabMzxmlMS1"
      ]
    },
    {
      "page": "grabMzxmlMS2",
      "title": "Extract the MS2 data from an mzXML nodeset",
      "topics": [
        "grabMzxmlMS2"
      ]
    },
    {
      "page": "grabMzxmlMS3",
      "title": "Extract the MS3 data from an mzXML nodeset",
      "topics": [
        "grabMzxmlMS3"
      ]
    },
    {
      "page": "grabMzxmlSpectraMzInt",
      "title": "Extract the mass-to-charge data from the spectra of an mzXML nodeset",
      "topics": [
        "grabMzxmlSpectraMzInt"
      ]
    },
    {
      "page": "grabMzxmlSpectraPremz",
      "title": "Extract the precursor mass from the spectra of an mzXML nodeset",
      "topics": [
        "grabMzxmlSpectraPremz"
      ]
    },
    {
      "page": "grabMzxmlSpectraRt",
      "title": "Extract the retention time from the spectra of an mzXML nodeset",
      "topics": [
        "grabMzxmlSpectraRt"
      ]
    },
    {
      "page": "grabMzxmlSpectraVoltage",
      "title": "Extract the collision energies from the spectra of an mzXML nodeset",
      "topics": [
        "grabMzxmlSpectraVoltage"
      ]
    },
    {
      "page": "grabSpectraInt",
      "title": "Extract the intensity information from the spectra of an mzML nodeset",
      "topics": [
        "grabSpectraInt"
      ]
    },
    {
      "page": "grabSpectraMz",
      "title": "Extract the mass-to-charge data from the spectra of an mzML nodeset",
      "topics": [
        "grabSpectraMz"
      ]
    },
    {
      "page": "grabSpectraPremz",
      "title": "Extract the precursor mass from the spectra of an mzML nodeset",
      "topics": [
        "grabSpectraPremz"
      ]
    },
    {
      "page": "grabSpectraRt",
      "title": "Extract the retention time from the spectra of an mzML nodeset",
      "topics": [
        "grabSpectraRt"
      ]
    },
    {
      "page": "grabSpectraVoltage",
      "title": "Extract the collision energies from the spectra of an mzML nodeset",
      "topics": [
        "grabSpectraVoltage"
      ]
    },
    {
      "page": "minifyMSdata",
      "title": "Shrink MS data by including only data points near masses of interest",
      "topics": [
        "minifyMSdata"
      ]
    },
    {
      "page": "minifyMzml",
      "title": "Shrink mzML files by including only data points near masses of interest",
      "topics": [
        "minifyMzml"
      ]
    },
    {
      "page": "minifyMzxml",
      "title": "Shrink mzXML files by including only data points near masses of interest",
      "topics": [
        "minifyMzxml"
      ]
    },
    {
      "page": "msdata_connection",
      "title": "S3 constructor for msdata_connection",
      "topics": [
        "msdata_connection"
      ]
    },
    {
      "page": "mz_group",
      "title": "Group m/z values into bins of a specified ppm width",
      "topics": [
        "mz_group"
      ]
    },
    {
      "page": "node2dt",
      "title": "Convert node to data.table",
      "topics": [
        "node2dt"
      ]
    },
    {
      "page": "pmppm",
      "title": "Plus/minus parts per million",
      "topics": [
        "pmppm"
      ]
    },
    {
      "page": "pmppm_vec",
      "title": "Plus/minus parts per million for multiple masses",
      "topics": [
        "pmppm_vec"
      ]
    },
    {
      "page": "print.msdata_connection",
      "title": "S3 print option for msdata_connection objects",
      "topics": [
        "print.msdata_connection"
      ]
    },
    {
      "page": "qplotMS1data",
      "title": "Quick plot for MS data",
      "topics": [
        "qplotMS1data"
      ]
    },
    {
      "page": "qplotMS2data",
      "title": "Quick plot for MS2 data",
      "topics": [
        "qplotMS2data"
      ]
    },
    {
      "page": "tmzmlMaker",
      "title": "Maker of tmzML documents",
      "topics": [
        "tmzmlMaker"
      ]
    },
    {
      "page": "trapz",
      "title": "Trapezoidal integration of mass-spec retention time / intensity values",
      "topics": [
        "trapz"
      ]
    }
  ],
  "_readme": "https://github.com/wkumler/rams/raw/HEAD/README.md",
  "_rundeps": [
    "base64enc",
    "cli",
    "data.table",
    "rlang",
    "xml2"
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      "source": "speed_size_comparison.Rmd",
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      "author": "William Kumler",
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      "headings": [
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        "RaMS package",
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        "Moving along: MSn data",
        "Continuing: chromatograms!",
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        "Saving space: EICs and rtrange",
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        "Getting started with tmzML documents",
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      "created": "2022-04-08 19:28:35",
      "modified": "2024-10-09 00:12:39",
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      "created": "2022-04-08 19:45:14",
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      "engine": "knitr::rmarkdown",
      "headings": [
        "Standard export to CSV",
        "Fancier export to Excel",
        "Exporting to SQL database",
        "Interfacing with Python via reticulate",
        "R code chunk:",
        "Python code chunk:"
      ],
      "created": "2021-01-31 22:09:31",
      "modified": "2024-03-03 02:04:15",
      "commits": 11
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