hidden_aliases {Spectra} | R Documentation

## Internal page for hidden aliases

### Description

For S4 methods that require a documentation entry but only clutter the index.

### Usage

    addProcessing(object, ...)

    backendInitialize(object, ...)

    backendMerge(object, ...)

    bin(x, ...)

    ## S4 method for signature 'numeric'
    bin(
      x,
      y,
      size = 1,
      breaks = seq(floor(min(y)), ceiling(max(y)), by = size),
      FUN = max
    )

    compareSpectra(x, y, ...)

    containsMz(object, ...)

    containsNeutralLoss(object, ...)

    dropNaSpectraVariables(object, ...)

    export(object, ...)

    filterMzRange(object, ...)

    filterMzValues(object, ...)

    isReadOnly(object, ...)

    peaksData(object, ...)

    peaksData(object) <- value

    pickPeaks(object, ...)

    replaceIntensitiesBelow(object, threshold = min, ...)

    reset(object, ...)

    selectSpectraVariables(object, ...)

    setBackend(object, backend, ...)

    spectrapply(object, ...)

    ## S4 method for signature 'MsBackendDataFrame'
    show(object)

    ## S4 method for signature 'MsBackendDataFrame'
    backendMerge(object, ...)

    ## S4 method for signature 'MsBackendDataFrame'
    acquisitionNum(object)

    ## S4 method for signature 'MsBackendDataFrame'
    peaksData(object)

    ## S4 method for signature 'MsBackendDataFrame'
    centroided(object)

    ## S4 replacement method for signature 'MsBackendDataFrame'
    centroided(object) <- value

    ## S4 method for signature 'MsBackendDataFrame'
    collisionEnergy(object)

    ## S4 replacement method for signature 'MsBackendDataFrame'
    collisionEnergy(object) <- value

    ## S4 method for signature 'MsBackendDataFrame'
    dataOrigin(object)

    ## S4 replacement method for signature 'MsBackendDataFrame'
    dataOrigin(object) <- value

    ## S4 method for signature 'MsBackendDataFrame'
    dataStorage(object)

    ## S4 replacement method for signature 'MsBackendDataFrame'
    dataStorage(object) <- value

    ## S4 method for signature 'MsBackendDataFrame'
    intensity(object)

    ## S4 replacement method for signature 'MsBackendDataFrame'
    intensity(object) <- value

    ## S4 method for signature 'MsBackendDataFrame'
    ionCount(object)

    ## S4 method for signature 'MsBackendDataFrame'
    isCentroided(object, ...)

    ## S4 method for signature 'MsBackendDataFrame'
    isEmpty(x)

    ## S4 method for signature 'MsBackendDataFrame'
    isolationWindowLowerMz(object)

    ## S4 replacement method for signature 'MsBackendDataFrame'
    isolationWindowLowerMz(object) <- value

    ## S4 method for signature 'MsBackendDataFrame'
    isolationWindowTargetMz(object)

    ## S4 replacement method for signature 'MsBackendDataFrame'
    isolationWindowTargetMz(object) <- value

    ## S4 method for signature 'MsBackendDataFrame'
    isolationWindowUpperMz(object)

    ## S4 replacement method for signature 'MsBackendDataFrame'
    isolationWindowUpperMz(object) <- value

    ## S4 method for signature 'MsBackendDataFrame'
    length(x)

    ## S4 method for signature 'MsBackendDataFrame'
    lengths(x, use.names = FALSE)

    ## S4 method for signature 'MsBackendDataFrame'
    msLevel(object, ...)

    ## S4 method for signature 'MsBackendDataFrame'
    mz(object)

    ## S4 replacement method for signature 'MsBackendDataFrame'
    mz(object) <- value

    ## S4 method for signature 'MsBackendDataFrame'
    polarity(object)

    ## S4 replacement method for signature 'MsBackendDataFrame'
    polarity(object) <- value

    ## S4 method for signature 'MsBackendDataFrame'
    precScanNum(object)

    ## S4 method for signature 'MsBackendDataFrame'
    precursorCharge(object)

    ## S4 method for signature 'MsBackendDataFrame'
    precursorIntensity(object)

    ## S4 method for signature 'MsBackendDataFrame'
    precursorMz(object)

    ## S4 replacement method for signature 'MsBackendDataFrame'
    peaksData(object) <- value

    ## S4 method for signature 'MsBackendDataFrame'
    rtime(object)

    ## S4 replacement method for signature 'MsBackendDataFrame'
    rtime(object) <- value

    ## S4 method for signature 'MsBackendDataFrame'
    scanIndex(object)

    ## S4 method for signature 'MsBackendDataFrame'
    selectSpectraVariables(object, spectraVariables = spectraVariables(object))

    ## S4 method for signature 'MsBackendDataFrame'
    smoothed(object)

    ## S4 replacement method for signature 'MsBackendDataFrame'
    smoothed(object) <- value

    ## S4 method for signature 'MsBackendDataFrame'
    spectraData(object, columns = spectraVariables(object))

    ## S4 replacement method for signature 'MsBackendDataFrame'
    spectraData(object) <- value

    ## S4 method for signature 'MsBackendDataFrame'
    spectraNames(object)

    ## S4 replacement method for signature 'MsBackendDataFrame'
    spectraNames(object) <- value

    ## S4 method for signature 'MsBackendDataFrame'
    spectraVariables(object)

    ## S4 method for signature 'MsBackendDataFrame'
    tic(object, initial = TRUE)

    ## S4 method for signature 'MsBackendDataFrame'
    x$name

    ## S4 replacement method for signature 'MsBackendDataFrame'
    x$name <- value

    ## S4 method for signature 'MsBackendDataFrame'
    x[i, j, ..., drop = FALSE]

    ## S4 method for signature 'MsBackendDataFrame,ANY'
    split(x, f, drop = FALSE, ...)

    ## S4 method for signature 'MsBackendDataFrame'
    filterAcquisitionNum(
      object,
      n = integer(),
      dataStorage = character(),
      dataOrigin = character()
    )

    ## S4 method for signature 'MsBackendHdf5Peaks'
    backendInitialize(
      object,
      files = character(),
      data = DataFrame(),
      hdf5path = character(),
      ...,
      BPPARAM = bpparam()
    )

    ## S4 method for signature 'MsBackendHdf5Peaks'
    show(object)

    ## S4 method for signature 'MsBackendHdf5Peaks'
    peaksData(object)

    ## S4 method for signature 'MsBackendHdf5Peaks'
    intensity(object)

    ## S4 replacement method for signature 'MsBackendHdf5Peaks'
    intensity(object) <- value

    ## S4 method for signature 'MsBackendHdf5Peaks'
    ionCount(object)

    ## S4 method for signature 'MsBackendHdf5Peaks'
    isCentroided(object, ...)

    ## S4 method for signature 'MsBackendHdf5Peaks'
    isEmpty(x)

    ## S4 method for signature 'MsBackendHdf5Peaks'
    lengths(x, use.names = FALSE)

    ## S4 method for signature 'MsBackendHdf5Peaks'
    mz(object)

    ## S4 replacement method for signature 'MsBackendHdf5Peaks'
    mz(object) <- value

    ## S4 replacement method for signature 'MsBackendHdf5Peaks'
    peaksData(object) <- value

    ## S4 method for signature 'MsBackendHdf5Peaks'
    spectraData(object, columns = spectraVariables(object))

    ## S4 replacement method for signature 'MsBackendHdf5Peaks'
    spectraData(object) <- value

    ## S4 replacement method for signature 'MsBackendHdf5Peaks'
    x$name <- value

    ## S4 method for signature 'MsBackendHdf5Peaks'
    x[i, j, ..., drop = FALSE]

    ## S4 method for signature 'MsBackendHdf5Peaks'
    backendMerge(object, ...)

    ## S4 method for signature 'MsBackendMzR'
    backendInitialize(object, files, ..., BPPARAM = bpparam())

    ## S4 method for signature 'MsBackendMzR'
    show(object)

    ## S4 method for signature 'MsBackendMzR'
    peaksData(object)

    ## S4 method for signature 'MsBackendMzR'
    intensity(object)

    ## S4 replacement method for signature 'MsBackendMzR'
    intensity(object) <- value

    ## S4 method for signature 'MsBackendMzR'
    ionCount(object)

    ## S4 method for signature 'MsBackendMzR'
    isCentroided(object, ...)

    ## S4 method for signature 'MsBackendMzR'
    isEmpty(x)

    ## S4 method for signature 'MsBackendMzR'
    lengths(x, use.names = FALSE)

    ## S4 method for signature 'MsBackendMzR'
    mz(object)

    ## S4 replacement method for signature 'MsBackendMzR'
    mz(object) <- value

    ## S4 method for signature 'MsBackendMzR'
    spectraData(object, columns = spectraVariables(object))

    ## S4 replacement method for signature 'MsBackendMzR'
    spectraData(object) <- value

    ## S4 method for signature 'MsBackendMzR'
    spectraNames(object)

    ## S4 replacement method for signature 'MsBackendMzR'
    spectraNames(object) <- value

    ## S4 method for signature 'MsBackendMzR'
    spectraVariables(object)

    ## S4 replacement method for signature 'MsBackendMzR'
    x$name <- value

    ## S4 method for signature 'MsBackendMzR'
    export(
      object,
      x,
      file = tempfile(),
      format = c("mzML", "mzXML"),
      copy = FALSE,
      BPPARAM = bpparam()
    )

    ## S4 method for signature 'Spectra'
    show(object)

### Value

Not applicable

[Package Spectra version 1.2.2 Index]