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  "_rbuild": "4.6.2",
  "_assets": [
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    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/contents.json",
    "extra/manual.pdf",
    "extra/NEWS.html",
    "extra/NEWS.txt",
    "extra/readme.html",
    "extra/readme.md",
    "extra/Spectra.html"
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  "_homeurl": "https://github.com/rformassspectrometry/spectra",
  "_realowner": "bioc",
  "_cranurl": false,
  "_exports": [
    "acquisitionNum",
    "addProcessing",
    "applyProcessing",
    "asDataFrame",
    "backendBpparam",
    "backendInitialize",
    "backendMerge",
    "backendParallelFactor",
    "backendRequiredSpectraVariables",
    "bin",
    "cbind2",
    "centroided",
    "centroided<-",
    "chunkapply",
    "collisionEnergy",
    "collisionEnergy<-",
    "combinePeaks",
    "combinePeaksData",
    "combineSpectra",
    "compareSpectra",
    "computeMzDeltas",
    "concatenateSpectra",
    "containsMz",
    "containsNeutralLoss",
    "coreSpectraVariables",
    "countIdentifications",
    "dataOrigin",
    "dataOrigin<-",
    "dataStorage",
    "dataStorage<-",
    "dataStorageBasePath",
    "dataStorageBasePath<-",
    "deisotopeSpectra",
    "dropNaSpectraVariables",
    "entropy",
    "estimatePrecursorIntensity",
    "estimatePrecursorMz",
    "export",
    "extractByIndex",
    "fillCoreSpectraVariables",
    "filterAcquisitionNum",
    "filterDataOrigin",
    "filterDataStorage",
    "filterEmptySpectra",
    "filterFourierTransformArtefacts",
    "filterIntensity",
    "filterIsolationWindow",
    "filterMsLevel",
    "filterMzRange",
    "filterMzValues",
    "filterNoisePeaks",
    "filterPeaksRanges",
    "filterPolarity",
    "filterPrecursorCharge",
    "filterPrecursorIsotopes",
    "filterPrecursorMaxIntensity",
    "filterPrecursorMz",
    "filterPrecursorMzRange",
    "filterPrecursorMzValues",
    "filterPrecursorPeaks",
    "filterPrecursorScan",
    "filterRanges",
    "filterRt",
    "filterValues",
    "fragmentGroupIndex",
    "intensity",
    "intensity<-",
    "ionCount",
    "isCentroided",
    "isEmpty",
    "isolationWindowLowerMz",
    "isolationWindowLowerMz<-",
    "isolationWindowTargetMz",
    "isolationWindowTargetMz<-",
    "isolationWindowUpperMz",
    "isolationWindowUpperMz<-",
    "isReadOnly",
    "joinPeaks",
    "joinPeaksGnps",
    "joinPeaksNone",
    "joinSpectraData",
    "longForm",
    "MsBackendCached",
    "MsBackendDataFrame",
    "MsBackendHdf5Peaks",
    "MsBackendMemory",
    "MsBackendMzR",
    "msLevel",
    "msLevel<-",
    "mz",
    "mz<-",
    "neutralLoss",
    "peaksData",
    "peaksData<-",
    "peaksVariables",
    "pickPeaks",
    "plotMzDelta",
    "plotSpectra",
    "plotSpectraMirror",
    "plotSpectraOverlay",
    "polarity",
    "polarity<-",
    "ppm",
    "precScanNum",
    "precursorCharge",
    "precursorIntensity",
    "precursorMz",
    "precursorMz<-",
    "PrecursorMzParam",
    "precursorPurity",
    "processingChunkFactor",
    "processingChunkSize",
    "processingChunkSize<-",
    "processingLog",
    "rbindlistWithRownames",
    "reduceSpectra",
    "replaceIntensitiesBelow",
    "reset",
    "rtime",
    "rtime<-",
    "scalePeaks",
    "scanIndex",
    "selectSpectraVariables",
    "setBackend",
    "shiftPeaks",
    "show",
    "smooth",
    "smoothed",
    "smoothed<-",
    "Spectra",
    "spectraData",
    "spectraData<-",
    "spectraNames",
    "spectraNames<-",
    "spectrapply",
    "spectraVariableMapping",
    "spectraVariableMapping<-",
    "spectraVariables",
    "split",
    "supportsSetBackend",
    "tic",
    "uniqueMsLevels"
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  "_datasets": [
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      "name": "fft_spectrum",
      "title": "Fast fourier transform artefact filter",
      "object": "fft_spectrum",
      "file": "fft_spectrum.RData",
      "class": [
        "Spectra"
      ],
      "fields": [],
      "table": false,
      "tojson": false
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  ],
  "_help": [
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      "page": "chunkapply",
      "title": "Apply a function stepwise to chunks of data",
      "topics": [
        "chunkapply"
      ]
    },
    {
      "page": "combinePeaks",
      "title": "Aggregating and combining mass peaks data",
      "topics": [
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        "combinePeaks,Spectra-method"
      ]
    },
    {
      "page": "combinePeaksData",
      "title": "Combine peaks with similar m/z across spectra",
      "concept": [
        "peak matrix combining functions"
      ],
      "topics": [
        "combinePeaksData"
      ]
    },
    {
      "page": "compareSpectra",
      "title": "Spectra similarity calculations",
      "topics": [
        "compareSpectra",
        "compareSpectra,Spectra,missing-method",
        "compareSpectra,Spectra,Spectra-method"
      ]
    },
    {
      "page": "combineSpectra",
      "title": "Merging, aggregating and splitting Spectra",
      "topics": [
        "c,Spectra-method",
        "cbind2",
        "cbind2,Spectra,dataframeOrDataFrameOrmatrix-method",
        "combineSpectra",
        "concatenateSpectra",
        "joinSpectraData",
        "split",
        "split,Spectra,ANY-method"
      ]
    },
    {
      "page": "countIdentifications",
      "title": "Count the number of identifications per scan",
      "topics": [
        "countIdentifications"
      ]
    },
    {
      "page": "filterMsLevel",
      "title": "Filter and subset Spectra objects",
      "topics": [
        "deisotopeSpectra",
        "dropNaSpectraVariables",
        "dropNaSpectraVariables,Spectra-method",
        "filterAcquisitionNum",
        "filterAcquisitionNum,Spectra-method",
        "filterDataOrigin",
        "filterDataOrigin,Spectra-method",
        "filterDataStorage",
        "filterDataStorage,Spectra-method",
        "filterEmptySpectra",
        "filterEmptySpectra,Spectra-method",
        "filterFourierTransformArtefacts,Spectra-method",
        "filterIntensity",
        "filterIntensity,Spectra-method",
        "filterIsolationWindow",
        "filterIsolationWindow,Spectra-method",
        "filterMsLevel",
        "filterMsLevel,Spectra-method",
        "filterMzRange",
        "filterMzRange,Spectra-method",
        "filterMzValues",
        "filterMzValues,Spectra-method",
        "filterPolarity",
        "filterPolarity,Spectra-method",
        "filterPrecursorCharge",
        "filterPrecursorCharge,Spectra-method",
        "filterPrecursorIsotopes",
        "filterPrecursorMaxIntensity",
        "filterPrecursorMz,Spectra-method",
        "filterPrecursorMzRange",
        "filterPrecursorMzRange,Spectra-method",
        "filterPrecursorMzValues",
        "filterPrecursorMzValues,Spectra-method",
        "filterPrecursorPeaks",
        "filterPrecursorScan",
        "filterPrecursorScan,Spectra-method",
        "filterRanges",
        "filterRanges,Spectra-method",
        "filterRt",
        "filterRt,Spectra-method",
        "filterValues",
        "filterValues,Spectra-method",
        "reduceSpectra",
        "selectSpectraVariables",
        "selectSpectraVariables,Spectra-method",
        "[,Spectra-method"
      ]
    },
    {
      "page": "estimatePrecursorIntensity",
      "title": "Estimate Precursor Intensities",
      "topics": [
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        "estimatePrecursorIntensity,Spectra-method"
      ]
    },
    {
      "page": "estimatePrecursorMz",
      "title": "Estimating precursor m/z valus for DDA data",
      "topics": [
        "estimatePrecursorMz"
      ]
    },
    {
      "page": "fillCoreSpectraVariables",
      "title": "Fill spectra data with columns for missing core variables",
      "topics": [
        "fillCoreSpectraVariables"
      ]
    },
    {
      "page": "filterFourierTransformArtefacts",
      "title": "Fast fourier transform artefact filter",
      "topics": [
        "fft_spectrum",
        "filterFourierTransformArtefacts"
      ]
    },
    {
      "page": "filterNoisePeaks",
      "title": "Filter peaks based on noise modeling",
      "topics": [
        "filterNoisePeaks"
      ]
    },
    {
      "page": "filterPeaksRanges",
      "title": "Filter peaks based on spectra and peaks variable ranges",
      "topics": [
        "filterPeaksRanges"
      ]
    },
    {
      "page": "fragmentGroupIndex",
      "title": "Mass fragmentation collections of each full scan",
      "topics": [
        "fragmentGroupIndex"
      ]
    },
    {
      "page": "joinPeaks",
      "title": "Join (map) peaks of two spectra",
      "topics": [
        "joinPeaks",
        "joinPeaksGnps",
        "joinPeaksNone"
      ]
    },
    {
      "page": "MsBackend",
      "title": "Mass spectrometry data backends",
      "topics": [
        "$,MsBackend-method",
        "$<-,MsBackend-method",
        "acquisitionNum,MsBackend-method",
        "backendBpparam",
        "backendBpparam,MsBackend-method",
        "backendInitialize",
        "backendInitialize,MsBackend-method",
        "backendInitialize,MsBackendDataFrame-method",
        "backendInitialize,MsBackendMemory-method",
        "backendMerge,list-method",
        "backendMerge,MsBackend-method",
        "backendParallelFactor",
        "backendParallelFactor,MsBackend-method",
        "backendParallelFactor,MsBackendHdf5Peaks-method",
        "backendParallelFactor,MsBackendMzR-method",
        "backendRequiredSpectraVariables",
        "backendRequiredSpectraVariables,MsBackend-method",
        "cbind2,MsBackend,dataframeOrDataFrameOrmatrix-method",
        "centroided,MsBackend-method",
        "centroided<-,MsBackend-method",
        "class:MsBackend",
        "collisionEnergy,MsBackend-method",
        "collisionEnergy<-,MsBackend-method",
        "dataOrigin,MsBackend-method",
        "dataOrigin<-,MsBackend-method",
        "dataStorage,MsBackend-method",
        "dataStorage<-,MsBackend-method",
        "dataStorageBasePath",
        "dataStorageBasePath,MsBackend-method",
        "dataStorageBasePath,MsBackendMzR-method",
        "dataStorageBasePath<-",
        "dataStorageBasePath<-,MsBackend-method",
        "dataStorageBasePath<-,MsBackendMzR-method",
        "dropNaSpectraVariables,MsBackend-method",
        "export,MsBackend-method",
        "extractByIndex",
        "extractByIndex,MsBackend,ANY-method",
        "extractByIndex,MsBackend,missing-method",
        "filterAcquisitionNum,MsBackend-method",
        "filterDataOrigin,MsBackend-method",
        "filterDataStorage,MsBackend-method",
        "filterEmptySpectra,MsBackend-method",
        "filterIsolationWindow,MsBackend-method",
        "filterMsLevel,MsBackend-method",
        "filterPolarity,MsBackend-method",
        "filterPrecursorCharge,MsBackend-method",
        "filterPrecursorMz,MsBackend-method",
        "filterPrecursorMzRange,MsBackend-method",
        "filterPrecursorMzValues,MsBackend-method",
        "filterPrecursorScan,MsBackend-method",
        "filterRanges,MsBackend-method",
        "filterRt,MsBackend-method",
        "filterValues,MsBackend-method",
        "intensity,MsBackend-method",
        "intensity<-,MsBackend-method",
        "ionCount,MsBackend-method",
        "isCentroided,MsBackend-method",
        "isEmpty,MsBackend-method",
        "isolationWindowLowerMz,MsBackend-method",
        "isolationWindowLowerMz<-,MsBackend-method",
        "isolationWindowTargetMz,MsBackend-method",
        "isolationWindowTargetMz<-,MsBackend-method",
        "isolationWindowUpperMz,MsBackend-method",
        "isolationWindowUpperMz<-,MsBackend-method",
        "isReadOnly,MsBackend-method",
        "length,MsBackend-method",
        "lengths,MsBackend-method",
        "longForm,MsBackend-method",
        "MsBackend",
        "MsBackend-class",
        "MsBackendDataFrame",
        "MsBackendDataFrame-class",
        "MsBackendHdf5Peaks",
        "MsBackendHdf5Peaks-class",
        "MsBackendMemory",
        "MsBackendMemory-class",
        "MsBackendMzR",
        "MsBackendMzR-class",
        "msLevel,MsBackend-method",
        "msLeveL<-,MsBackend-method",
        "msLevel<-,MsBackend-method",
        "mz,MsBackend-method",
        "mz<-,MsBackend-method",
        "peaksData,MsBackend-method",
        "peaksData<-,MsBackend-method",
        "peaksVariables,MsBackend-method",
        "polarity,MsBackend-method",
        "polarity<-,MsBackend-method",
        "precScanNum,MsBackend-method",
        "precursorCharge,MsBackend-method",
        "precursorIntensity,MsBackend-method",
        "precursorMz,MsBackend-method",
        "precursorMz<-,MsBackend-method",
        "reset,MsBackend-method",
        "rtime,MsBackend-method",
        "rtime<-,MsBackend-method",
        "scanIndex,MsBackend-method",
        "selectSpectraVariables,MsBackend-method",
        "smoothed,MsBackend-method",
        "smoothed<-,MsBackend-method",
        "spectraData,MsBackend-method",
        "spectraData<-,MsBackend-method",
        "spectraNames,MsBackend-method",
        "spectraNames<-,MsBackend-method",
        "spectraVariables,MsBackend-method",
        "split,MsBackend,ANY-method",
        "supportsSetBackend",
        "supportsSetBackend,MsBackend-method",
        "tic,MsBackend-method",
        "uniqueMsLevels,MsBackend-method",
        "[,MsBackend-method",
        "[[,MsBackend-method",
        "[[<-,MsBackend-method"
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    },
    {
      "page": "MsBackendCached",
      "title": "Base MsBackend class providing data caching mechanism",
      "topics": [
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        "$<-,MsBackendCached-method",
        "backendInitialize,MsBackendCached-method",
        "dataStorage,MsBackendCached-method",
        "extractByIndex,MsBackendCached,ANY-method",
        "intensity,MsBackendCached-method",
        "ionCount,MsBackendCached-method",
        "length,MsBackendCached-method",
        "MsBackendCached",
        "MsBackendCached-class",
        "mz,MsBackendCached-method",
        "selectSpectraVariables,MsBackendCached-method",
        "show,MsBackendCached-method",
        "spectraData,MsBackendCached-method",
        "spectraData<-,MsBackendCached-method",
        "spectraVariables,MsBackendCached-method",
        "[,MsBackendCached-method"
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    },
    {
      "page": "neutralLoss",
      "title": "Calculate Neutral Loss Spectra",
      "topics": [
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        "neutralLoss,Spectra,PrecursorMzParam-method",
        "PrecursorMzParam"
      ]
    },
    {
      "page": "plotMzDelta",
      "title": "MZ delta Quality Control",
      "topics": [
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        "plotMzDelta"
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    },
    {
      "page": "precursorPurity",
      "title": "Calculating Precursor Purity for MS2 spectra",
      "topics": [
        "precursorPurity"
      ]
    },
    {
      "page": "processingChunkSize",
      "title": "Parallel and chunk-wise processing of 'Spectra'",
      "topics": [
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        "processingChunkFactor",
        "processingChunkFactor,Spectra-method",
        "processingChunkSize",
        "processingChunkSize,Spectra-method",
        "processingChunkSize<-",
        "processingChunkSize<-,Spectra-method"
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    },
    {
      "page": "addProcessing",
      "title": "Data manipulation and analysis methods",
      "topics": [
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        "addProcessing,Spectra-method",
        "applyProcessing",
        "applyProcessing,Spectra-method",
        "bin",
        "bin,Spectra-method",
        "containsMz",
        "containsMz,Spectra-method",
        "containsNeutralLoss",
        "containsNeutralLoss,Spectra-method",
        "entropy",
        "entropy,ANY-method",
        "entropy,Spectra-method",
        "pickPeaks",
        "pickPeaks,Spectra-method",
        "processingLog",
        "replaceIntensitiesBelow",
        "replaceIntensitiesBelow,Spectra-method",
        "reset",
        "reset,Spectra-method",
        "scalePeaks",
        "shiftPeaks",
        "smooth",
        "smooth,Spectra-method",
        "spectrapply",
        "spectrapply,Spectra-method"
      ]
    },
    {
      "page": "rbindlistWithRownames",
      "title": "Fast _rbind-ing_ 'data.frame's preserving row names",
      "topics": [
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      ]
    },
    {
      "page": "Spectra",
      "title": "The Spectra class to manage and access MS data",
      "topics": [
        "dataStorageBasePath,Spectra-method",
        "dataStorageBasePath<-,Spectra-method",
        "export",
        "export,Spectra-method",
        "setBackend",
        "setBackend,Spectra,MsBackend-method",
        "Spectra",
        "Spectra,ANY-method",
        "Spectra,character-method",
        "Spectra,missing-method",
        "Spectra,MsBackend-method",
        "Spectra-class"
      ]
    },
    {
      "page": "spectra-plotting",
      "title": "Plotting Spectra",
      "topics": [
        "plotSpectra",
        "plotSpectraMirror",
        "plotSpectraMirror,Spectra-method",
        "plotSpectraOverlay",
        "spectra-plotting"
      ]
    },
    {
      "page": "spectraData",
      "title": "Accessing mass spectrometry data",
      "topics": [
        "$,Spectra-method",
        "$<-,Spectra-method",
        "acquisitionNum",
        "acquisitionNum,Spectra-method",
        "asDataFrame",
        "centroided",
        "centroided,Spectra-method",
        "centroided<-,Spectra-method",
        "collisionEnergy",
        "collisionEnergy,Spectra-method",
        "collisionEnergy<-,Spectra-method",
        "coreSpectraVariables",
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        "dataOrigin,Spectra-method",
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      "page": "spectraVariableMapping",
      "title": "Mapping between spectra variables and data file fields",
      "topics": [
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        "spectraVariableMapping,Spectra-method",
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