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Internal page for hidden aliases

Source: R/hidden_aliases.R, R/AllGenerics.R, R/MsBackendDataFrame.R, and 4 more
hidden_aliases.Rd

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

Usage

# S4 method for numeric
bin(
  x,
  y,
  size = 1,
  breaks = seq(floor(min(y)), ceiling(max(y)), by = size),
  FUN = max,
  returnMids = TRUE,
  .check = TRUE
)

containsMz(object, ...)

containsNeutralLoss(object, ...)

dropNaSpectraVariables(object, ...)

entropy(object, ...)

export(object, ...)

pickPeaks(object, ...)

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

reset(object, ...)

selectSpectraVariables(object, ...)

# S4 method for MsBackendDataFrame
show(object)

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

# S4 method for MsBackendDataFrame
acquisitionNum(object)

# S4 method for MsBackendDataFrame
peaksData(object, columns = c("mz", "intensity"))

# S4 method for MsBackendDataFrame
centroided(object)

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

# S4 method for MsBackendDataFrame
collisionEnergy(object)

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

# S4 method for MsBackendDataFrame
dataOrigin(object)

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

# S4 method for MsBackendDataFrame
dataStorage(object)

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

# S4 method for MsBackendDataFrame
intensity(object)

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

# S4 method for MsBackendDataFrame
isEmpty(x)

# S4 method for MsBackendDataFrame
isolationWindowLowerMz(object)

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

# S4 method for MsBackendDataFrame
isolationWindowTargetMz(object)

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

# S4 method for MsBackendDataFrame
isolationWindowUpperMz(object)

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

# S4 method for MsBackendDataFrame
length(x)

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

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

# S4 method for MsBackendDataFrame
msLevel(object) <- value

# S4 method for MsBackendDataFrame
mz(object)

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

# S4 method for MsBackendDataFrame
polarity(object)

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

# S4 method for MsBackendDataFrame
precScanNum(object)

# S4 method for MsBackendDataFrame
precursorCharge(object)

# S4 method for MsBackendDataFrame
precursorIntensity(object)

# S4 method for MsBackendDataFrame
precursorMz(object)

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

# S4 method for MsBackendDataFrame
peaksVariables(object)

# S4 method for MsBackendDataFrame
rtime(object)

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

# S4 method for MsBackendDataFrame
scanIndex(object)

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

# S4 method for MsBackendDataFrame
smoothed(object)

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

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

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

# S4 method for MsBackendDataFrame
spectraNames(object)

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

# S4 method for MsBackendDataFrame
spectraVariables(object)

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

# S4 method for MsBackendDataFrame
$(x, name)

# S4 method for MsBackendDataFrame
$(x, name) <- value

# S4 method for MsBackendDataFrame
[(x, i, j, ..., drop = FALSE)

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

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

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

# S4 method for MsBackendHdf5Peaks
show(object)

# S4 method for MsBackendHdf5Peaks
peaksData(object, columns = peaksVariables(object))

# S4 method for MsBackendHdf5Peaks
intensity(object)

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

# S4 method for MsBackendHdf5Peaks
ionCount(object)

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

# S4 method for MsBackendHdf5Peaks
isEmpty(x)

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

# S4 method for MsBackendHdf5Peaks
mz(object)

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

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

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

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

# S4 method for MsBackendHdf5Peaks
$(x, name) <- value

# S4 method for MsBackendHdf5Peaks
[(x, i, j, ..., drop = FALSE)

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

# S4 method for MsBackendMemory
show(object)

# S4 method for MsBackendMemory
backendMerge(object, ...)

# S4 method for MsBackendMemory
acquisitionNum(object)

# S4 method for MsBackendMemory
centroided(object)

# S4 method for MsBackendMemory
centroided(object) <- value

# S4 method for MsBackendMemory
collisionEnergy(object)

# S4 method for MsBackendMemory
collisionEnergy(object) <- value

# S4 method for MsBackendMemory
dataOrigin(object)

# S4 method for MsBackendMemory
dataOrigin(object) <- value

# S4 method for MsBackendMemory
dataStorage(object)

# S4 method for MsBackendMemory
dataStorage(object) <- value

# S4 method for MsBackendMemory
intensity(object)

# S4 method for MsBackendMemory
intensity(object) <- value

# S4 method for MsBackendMemory
ionCount(object)

# S4 method for MsBackendMemory
isEmpty(x)

# S4 method for MsBackendMemory
isolationWindowLowerMz(object)

# S4 method for MsBackendMemory
isolationWindowLowerMz(object) <- value

# S4 method for MsBackendMemory
isolationWindowTargetMz(object)

# S4 method for MsBackendMemory
isolationWindowTargetMz(object) <- value

# S4 method for MsBackendMemory
isolationWindowUpperMz(object)

# S4 method for MsBackendMemory
isolationWindowUpperMz(object) <- value

# S4 method for MsBackendMemory
length(x)

# S4 method for MsBackendMemory
lengths(x, use.names = FALSE)

# S4 method for MsBackendMemory
msLevel(object, ...)

# S4 method for MsBackendMemory
msLevel(object) <- value

# S4 method for MsBackendMemory
mz(object)

# S4 method for MsBackendMemory
mz(object) <- value

# S4 method for MsBackendMemory
peaksData(object, columns = c("mz", "intensity"))

# S4 method for MsBackendMemory
peaksData(object) <- value

# S4 method for MsBackendMemory
polarity(object)

# S4 method for MsBackendMemory
polarity(object) <- value

# S4 method for MsBackendMemory
precScanNum(object)

# S4 method for MsBackendMemory
precursorCharge(object)

# S4 method for MsBackendMemory
precursorIntensity(object)

# S4 method for MsBackendMemory
precursorMz(object)

# S4 method for MsBackendMemory
rtime(object)

# S4 method for MsBackendMemory
rtime(object) <- value

# S4 method for MsBackendMemory
scanIndex(object)

# S4 method for MsBackendMemory
selectSpectraVariables(object, spectraVariables = spectraVariables(object))

# S4 method for MsBackendMemory
smoothed(object)

# S4 method for MsBackendMemory
smoothed(object) <- value

# S4 method for MsBackendMemory
spectraData(object, columns = spectraVariables(object))

# S4 method for MsBackendMemory
spectraData(object) <- value

# S4 method for MsBackendMemory
spectraNames(object)

# S4 method for MsBackendMemory
spectraNames(object) <- value

# S4 method for MsBackendMemory
spectraVariables(object)

# S4 method for MsBackendMemory
peaksVariables(object)

# S4 method for MsBackendMemory
tic(object, initial = TRUE)

# S4 method for MsBackendMemory
$(x, name)

# S4 method for MsBackendMemory
$(x, name) <- value

# S4 method for MsBackendMemory
[(x, i, j, ..., drop = FALSE)

# S4 method for MsBackendMemory,ANY
split(x, f, drop = FALSE, ...)

# S4 method for MsBackendMemory
filterAcquisitionNum(
  object,
  n = integer(),
  dataStorage = character(),
  dataOrigin = character()
)

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

# S4 method for MsBackendMzR
show(object)

# S4 method for MsBackendMzR
peaksData(object, columns = peaksVariables(object))

# S4 method for MsBackendMzR
intensity(object)

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

# S4 method for MsBackendMzR
ionCount(object)

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

# S4 method for MsBackendMzR
isEmpty(x)

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

# S4 method for MsBackendMzR
mz(object)

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

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

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

# S4 method for MsBackendMzR
spectraNames(object)

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

# S4 method for MsBackendMzR
spectraVariables(object)

# S4 method for MsBackendMzR
$(x, name) <- value

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

# S4 method for Spectra
show(object)

# S4 method for list
combinePeaks(object, ...)

Value

Not applicable

Note

: this replaces all the data in the backend.