{
  "_id": "6a196663acfb0bcc41de7482",
  "Package": "Chromatograms",
  "Title": "Infrastructure for Chromatographic Mass Spectrometry Data",
  "Version": "1.2.0",
  "Description": "The Chromatograms packages defines an efficient\ninfrastructure for storing and handling of chromatographic mass\nspectrometry data. It provides different implementations of\n*backends* to store and represent the data. Such backends can\nbe optimized for small memory footprint or fast data\naccess/processing. A lazy evaluation queue and chunk-wise\nprocessing capabilities ensure efficient analysis of also very\nlarge data sets.",
  "Authors@R": "c(person(given = \"Johannes\", family = \"Rainer\",\nemail = \"Johannes.Rainer@eurac.edu\",\nrole = c(\"aut\"),\ncomment = c(ORCID = \"0000-0002-6977-7147\")),\nperson(given = \"Laurent\", family = \"Gatto\",\ncomment = c(ORCID = \"0000-0002-1520-2268\"),\nemail = \"laurent.gatto@uclouvain.be\",\nrole = c(\"aut\")),\nperson(given = \"Philippine\", family = \"Louail\",\nemail = \"philippine.louail@outlook.com\",\nrole = c(\"aut\", \"cre\"),\ncomment = c(ORCID = \"0009-0007-5429-6846\",\nfnd = \"European Union HORIZON-MSCA-2021 project\nGrant No. 101073062: HUMAN – Harmonising and Unifying Blood\nMetabolic Analysis Networks\")))",
  "License": "Artistic-2.0",
  "Encoding": "UTF-8",
  "VignetteBuilder": "knitr",
  "BugReports": "https://github.com/RforMassSpectrometry/Chromatograms/issues",
  "URL": "https://github.com/RforMassSpectrometry/Chromatograms",
  "biocViews": "Infrastructure, Metabolomics, MassSpectrometry, Proteomics",
  "Roxygen": "list(markdown=TRUE)",
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  "Collate": "'AllGenerics.R' 'ChromBackend-functions.R' 'ChromBackend.R'\n'hidden_aliases.R' 'helpers.R' 'ChromBackendMemory.R'\n'ChromBackendMzR.R' 'ChromBackendSpectra.R' 'Chromatograms.R'\n'Chromatograms-chromData.R' 'Chromatograms-peaksData.R'\n'Chromatograms-plot.R' 'Chromatograms-processingQueue.R'",
  "Config/pak/sysreqs": "cmake make libuv1-dev",
  "Repository": "https://bioc-release.r-universe.dev",
  "Date/Publication": "2026-04-28 13:05:23 UTC",
  "RemoteUrl": "https://github.com/bioc/Chromatograms",
  "RemoteRef": "RELEASE_3_23",
  "RemoteSha": "afed21c2e832cf6697f63139ab5b958edbdd4100",
  "NeedsCompilation": "no",
  "Packaged": {
    "Date": "2026-05-29 08:10:56 UTC",
    "User": "root"
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  "Author": "Johannes Rainer [aut] (ORCID: <https://orcid.org/0000-0002-6977-7147>),\nLaurent Gatto [aut] (ORCID: <https://orcid.org/0000-0002-1520-2268>),\nPhilippine Louail [aut, cre] (ORCID:\n<https://orcid.org/0009-0007-5429-6846>, fnd: European Union\nHORIZON-MSCA-2021 project Grant No. 101073062: HUMAN – Harmonising\nand Unifying Blood Metabolic Analysis Networks)",
  "Maintainer": "Philippine Louail <philippine.louail@outlook.com>",
  "MD5sum": "1b505ca8562eed2d00324d02d9483727",
  "_user": "bioc-release",
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  "_created": "2026-05-29T08:10:56.000Z",
  "_published": "2026-05-29T10:11:47.817Z",
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    },
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      "version": "1.2.0",
      "bioc": "3.23"
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  "_topics": [
    "infrastructure",
    "metabolomics",
    "massspectrometry",
    "proteomics"
  ],
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  "_contributors": [
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      "user": "philouail",
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    "name": "Bioconductor",
    "description": "Software for the analysis and comprehension of high-throughput genomic data"
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    "count": 197,
    "source": "https://www.bioconductor.org/packages/stats/bioc/Chromatograms"
  },
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  "_rbuild": "4.6.0",
  "_assets": [
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    "extra/citation.cff",
    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/contents.json",
    "extra/readme.html",
    "extra/readme.md",
    "manual.pdf"
  ],
  "_homeurl": "https://github.com/rformassspectrometry/chromatograms",
  "_realowner": "bioc",
  "_cranurl": false,
  "_exports": [
    "applyProcessing",
    "backendBpparam",
    "backendInitialize",
    "backendMerge",
    "backendParallelFactor",
    "Chromatograms",
    "ChromBackendMemory",
    "ChromBackendMzR",
    "ChromBackendSpectra",
    "chromData",
    "chromData<-",
    "chromExtract",
    "chromIndex",
    "chromIndex<-",
    "chromSpectraIndex",
    "chromVariables",
    "collisionEnergy",
    "collisionEnergy<-",
    "compareChromatograms",
    "concatenateChromatograms",
    "coreChromVariables",
    "corePeaksVariables",
    "dataOrigin",
    "dataOrigin<-",
    "extractByIndex",
    "factorize",
    "fillCoreChromVariables",
    "filterChromData",
    "filterEmptyChromatograms",
    "filterPeaksData",
    "imputePeaksData",
    "intensity",
    "intensity<-",
    "isEmpty",
    "isReadOnly",
    "matchRtime",
    "msLevel",
    "msLevel<-",
    "mz",
    "mz<-",
    "mzMax",
    "mzMax<-",
    "mzMin",
    "mzMin<-",
    "peakBoundary",
    "peaksData",
    "peaksData<-",
    "plotChromatograms",
    "plotChromatogramsOverlay",
    "precursorMz",
    "precursorMz<-",
    "precursorMzMax",
    "precursorMzMax<-",
    "precursorMzMin",
    "precursorMzMin<-",
    "processingChunkFactor",
    "processingChunkSize",
    "processingChunkSize<-",
    "productMz",
    "productMz<-",
    "productMzMax",
    "productMzMax<-",
    "productMzMin",
    "productMzMin<-",
    "reset",
    "rtime",
    "rtime<-",
    "setBackend",
    "show",
    "split",
    "supportsSetBackend",
    "validChromData",
    "validPeaksData"
  ],
  "_help": [
    {
      "page": "Chromatograms",
      "title": "The Chromatograms class to manage and access chromatographic data",
      "topics": [
        "$,Chromatograms-method",
        "$<-,Chromatograms-method",
        "Chromatograms",
        "Chromatograms,ChromBackendOrMissing-method",
        "Chromatograms,Spectra-method",
        "Chromatograms-class",
        "chromExtract",
        "chromExtract,Chromatograms-method",
        "factorize,Chromatograms-method",
        "filterEmptyChromatograms",
        "filterEmptyChromatograms,Chromatograms-method",
        "setBackend,Chromatograms,ChromBackend-method",
        "[,Chromatograms-method",
        "[<-,Chromatograms-method",
        "[[,Chromatograms-method",
        "[[<-,Chromatograms-method"
      ]
    },
    {
      "page": "ChromBackendMemory",
      "title": "Improved in-memory Chromatographic data backend",
      "topics": [
        "backendInitialize,ChromBackendMemory-method",
        "ChromBackendMemory"
      ]
    },
    {
      "page": "ChromBackendMzR",
      "title": "Chromatographic Data Backend for Reading mzML Files",
      "topics": [
        "backendInitialize,ChromBackendMzR-method",
        "ChromBackendMzR"
      ]
    },
    {
      "page": "ChromBackendSpectra",
      "title": "Chromatographic Data Backend for Spectra Objects",
      "topics": [
        "backendInitialize,ChromBackendSpectra-method",
        "ChromBackendSpectra",
        "chromSpectraIndex"
      ]
    },
    {
      "page": "chromData",
      "title": "Chromatographic Peaks Metadata.",
      "topics": [
        "chromData",
        "chromData,Chromatograms-method",
        "chromData<-",
        "chromData<-,Chromatograms-method",
        "chromIndex",
        "chromIndex,Chromatograms-method",
        "chromIndex<-",
        "chromIndex<-,Chromatograms-method",
        "chromVariables",
        "chromVariables,Chromatograms-method",
        "chromVariables<-",
        "collisionEnergy",
        "collisionEnergy,Chromatograms-method",
        "collisionEnergy<-",
        "collisionEnergy<-,Chromatograms-method",
        "dataOrigin",
        "dataOrigin,Chromatograms-method",
        "dataOrigin<-",
        "dataOrigin<-,Chromatograms-method",
        "filterChromData",
        "filterChromData,Chromatograms-method",
        "length,Chromatograms-method",
        "msLevel",
        "msLevel,Chromatograms-method",
        "msLevel<-",
        "msLevel<-,Chromatograms-method",
        "mz",
        "mz,Chromatograms-method",
        "mz<-",
        "mz<-,Chromatograms-method",
        "mzMax",
        "mzMax,Chromatograms-method",
        "mzMax<-",
        "mzMax<-,Chromatograms-method",
        "mzMin",
        "mzMin,Chromatograms-method",
        "mzMin<-",
        "mzMin<-,Chromatograms-method",
        "precursorMz",
        "precursorMz,Chromatograms-method",
        "precursorMz<-",
        "precursorMz<-,Chromatograms-method",
        "precursorMzMax",
        "precursorMzMax,Chromatograms-method",
        "precursorMzMax<-",
        "precursorMzMax<-,Chromatograms-method",
        "precursorMzMin",
        "precursorMzMin,Chromatograms-method",
        "precursorMzMin<-",
        "precursorMzMin<-,Chromatograms-method",
        "productMz",
        "productMz,Chromatograms-method",
        "productMz<-",
        "productMz<-,Chromatograms-method",
        "productMzMax",
        "productMzMax,Chromatograms-method",
        "productMzMax<-",
        "productMzMax<-,Chromatograms-method",
        "productMzMin",
        "productMzMin,Chromatograms-method",
        "productMzMin<-",
        "productMzMin<-,Chromatograms-method"
      ]
    },
    {
      "page": "concatenateChromatograms",
      "title": "Merging, combining and splitting Chromatograms",
      "topics": [
        "c,Chromatograms-method",
        "concatenateChromatograms",
        "split,Chromatograms,ANY-method"
      ]
    },
    {
      "page": "ChromBackend",
      "title": "Chromatographic MS Data Backends",
      "topics": [
        "$,ChromBackend-method",
        "$<-,ChromBackend-method",
        "backendBpparam,ChromBackend-method",
        "backendInitialize,ChromBackend-method",
        "backendMerge,ChromBackend-method",
        "backendMerge,list-method",
        "backendParallelFactor,ChromBackend-method",
        "ChromBackend",
        "ChromBackend-class",
        "ChromBackendMemory-class",
        "ChromBackendMzR-class",
        "ChromBackendSpectra-class",
        "chromData,ChromBackend-method",
        "chromData<-,ChromBackend-method",
        "chromExtract,ChromBackend-method",
        "chromIndex,ChromBackend-method",
        "chromIndex<-,ChromBackend-method",
        "chromVariables,ChromBackend-method",
        "collisionEnergy,ChromBackend-method",
        "collisionEnergy<-,ChromBackend-method",
        "coreChromVariables",
        "corePeaksVariables",
        "dataOrigin,ChromBackend-method",
        "dataOrigin<-,ChromBackend-method",
        "extractByIndex",
        "extractByIndex,ChromBackend,ANY-method",
        "extractByIndex,ChromBackend,missing-method",
        "factorize",
        "factorize,ChromBackend-method",
        "filterChromData,ChromBackend-method",
        "filterEmptyChromatograms,ChromBackend-method",
        "filterPeaksData,ChromBackend-method",
        "imputePeaksData,ChromBackend-method",
        "intensity,ChromBackend-method",
        "intensity<-,ChromBackend-method",
        "isEmpty,ChromBackend-method",
        "isReadOnly,ChromBackend-method",
        "length,ChromBackend-method",
        "lengths,ChromBackend-method",
        "msLevel,ChromBackend-method",
        "msLevel<-,ChromBackend-method",
        "mz,ChromBackend-method",
        "mz<-,ChromBackend-method",
        "mzMax,ChromBackend-method",
        "mzMax<-,ChromBackend-method",
        "mzMin,ChromBackend-method",
        "mzMin<-,ChromBackend-method",
        "peaksData,ChromBackend-method",
        "peaksData<-,ChromBackend-method",
        "peaksVariables,ChromBackend-method",
        "precursorMz,ChromBackend-method",
        "precursorMz<-,ChromBackend-method",
        "precursorMzMax,ChromBackend-method",
        "precursorMzMax<-,ChromBackend-method",
        "precursorMzMin,ChromBackend-method",
        "precursorMzMin<-,ChromBackend-method",
        "productMz,ChromBackend-method",
        "productMz<-,ChromBackend-method",
        "productMzMax,ChromBackend-method",
        "productMzMax<-,ChromBackend-method",
        "productMzMin,ChromBackend-method",
        "productMzMin<-,ChromBackend-method",
        "reset,ChromBackend-method",
        "rtime,ChromBackend-method",
        "rtime<-,ChromBackend-method",
        "split,ChromBackend,ANY-method",
        "supportsSetBackend,ChromBackend-method",
        "[,ChromBackend-method",
        "[[,ChromBackend-method",
        "[[<-,ChromBackend-method"
      ]
    },
    {
      "page": "peaksData",
      "title": "Chromatographic peaks data",
      "topics": [
        "compareChromatograms",
        "compareChromatograms,Chromatograms,Chromatograms-method",
        "compareChromatograms,Chromatograms,missing-method",
        "filterPeaksData",
        "filterPeaksData,Chromatograms-method",
        "imputePeaksData",
        "imputePeaksData,Chromatograms-method",
        "intensity,Chromatograms-method",
        "intensity<-,Chromatograms-method",
        "lengths,Chromatograms-method",
        "matchRtime",
        "peakBoundary",
        "peakBoundary,Chromatograms-method",
        "peaksData",
        "peaksData,Chromatograms-method",
        "peaksData<-,Chromatograms-method",
        "peaksVariables",
        "peaksVariables,Chromatograms-method",
        "rtime,Chromatograms-method",
        "rtime<-,Chromatograms-method"
      ]
    },
    {
      "page": "plotChromatograms",
      "title": "Plot chromatograms",
      "topics": [
        "plotChromatograms",
        "plotChromatogramsOverlay"
      ]
    },
    {
      "page": "processingQueue",
      "title": "Efficiently processing 'Chromatograms' objects.",
      "topics": [
        "addProcessing,Chromatograms-method",
        "applyProcessing,Chromatograms-method",
        "processingChunkFactor,Chromatograms-method",
        "processingChunkSize,Chromatograms-method",
        "processingChunkSize<-,Chromatograms-method",
        "processingQueue"
      ]
    }
  ],
  "_readme": "https://github.com/bioc/Chromatograms/raw/RELEASE_3_23/README.md",
  "_rundeps": [
    "BH",
    "BiocGenerics",
    "BiocParallel",
    "clue",
    "cluster",
    "codetools",
    "cpp11",
    "data.table",
    "formatR",
    "fs",
    "futile.logger",
    "futile.options",
    "generics",
    "IRanges",
    "lambda.r",
    "MASS",
    "MetaboCoreUtils",
    "MsCoreUtils",
    "ProtGenerics",
    "Rcpp",
    "S4Vectors",
    "snow",
    "Spectra"
  ],
  "_vignettes": [
    {
      "source": "creating-backend-classes.Rmd",
      "filename": "creating-backend-classes.html",
      "title": "Creating new ChromBackend classes for Chromatograms",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Introduction",
        "What is a ChromBackend?",
        "Conventions and definitions",
        "Notes on parallel and chunk-wise processing",
        "API",
        "Required methods",
        "dataStorage()",
        "length()",
        "backendInitialize()",
        "chromVariables()",
        "chromData()",
        "peaksVariables()",
        "peaksData()",
        "[",
        "$",
        "backendMerge()",
        "Data replacement methods",
        "chromData<-",
        "$<-",
        "peaksData<-",
        "Methods with available default implementations",
        "backendParallelFactor()",
        "chromIndex()",
        "collisionEnergy()",
        "dataOrigin(), dataOrigin<-",
        "intensity(), intensity<-",
        "isEmpty()",
        "isReadOnly()",
        "lengths()",
        "msLevel(), msLevel<-",
        "mz(), mz<-",
        "mzMax(), mzMax<-",
        "mzMin(), mzMin<-`",
        "precursorMz(), precursorMz<-",
        "precursorMzMax(), precursorMzMax<-",
        "precursorMzMin(), precursorMzMin<-",
        "productMz(), productMz<-",
        "productMzMax(), productMzMax<-",
        "productMzMin(), productMzMin<-",
        "rtime(), rtime<-",
        "split()",
        "Session information"
      ],
      "created": "2024-03-27 07:29:10",
      "modified": "2025-07-14 12:10:13",
      "commits": 6
    },
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      "source": "using-a-chromatograms-object.Rmd",
      "filename": "using-a-chromatograms-object.html",
      "title": "Using and understanding a Chromatograms object",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Introduction",
        "Installation",
        "The Chromatograms object",
        "Available backends",
        "Chromatographic peaks data",
        "Chromatograms metadata",
        "Creating Chromatograms objects",
        "Access data from a Chromatograms object",
        "peaksData",
        "chromData",
        "Lazy Processing and Parallelization",
        "Processing queue",
        "Parallelization",
        "Changing backend type",
        "Choosing the right backend",
        "Plotting chromatograms from a Spectra object",
        "Understanding Factorization",
        "Re-factorizing after metadata changes",
        "Extracting chromatographic regions of interest",
        "Basic extraction by retention time",
        "Extraction with m/z filtering (ChromBackendSpectra only)",
        "Imputing missing values in chromatograms",
        "Available imputation methods",
        "Extrapolation vs. Interpolation",
        "Example: Imputing an extracted ion chromatogram (EIC)",
        "Selecting the right imputation method",
        "Imputation in lazy evaluation pipelines",
        "Comparing chromatograms",
        "Comparing chromatograms within a single object",
        "Comparing two Chromatograms objects",
        "Comparing groups of chromatograms",
        "Session information"
      ],
      "created": "2025-02-18 08:10:12",
      "modified": "2026-04-02 11:04:41",
      "commits": 10
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