Spectra Infrastructure for Mass Spectrometry Data

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Documentation for package ‘Spectra’ version 1.0.5

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A B C D E F I J L M P R S T misc

-- A --

acquisitionNum-method Mass spectrometry data backends
acquisitionNum-method The Spectra class to manage and access MS data
addProcessing The Spectra class to manage and access MS data
applyProcessing The Spectra class to manage and access MS data

-- B --

backendInitialize-method Mass spectrometry data backends
backendMerge-method Mass spectrometry data backends
bin-method The Spectra class to manage and access MS data

-- C --

c-method The Spectra class to manage and access MS data
centroided-method Mass spectrometry data backends
centroided-method The Spectra class to manage and access MS data
centroided<--method Mass spectrometry data backends
centroided<--method The Spectra class to manage and access MS data
class:MsBackend Mass spectrometry data backends
collisionEnergy-method Mass spectrometry data backends
collisionEnergy-method The Spectra class to manage and access MS data
collisionEnergy<--method Mass spectrometry data backends
collisionEnergy<--method The Spectra class to manage and access MS data
combinePeaks Combine peaks with similar m/z across spectra
combineSpectra The Spectra class to manage and access MS data
compareSpectra-method The Spectra class to manage and access MS data
containsMz-method The Spectra class to manage and access MS data
containsNeutralLoss-method The Spectra class to manage and access MS data

-- D --

dataOrigin-method Mass spectrometry data backends
dataOrigin-method The Spectra class to manage and access MS data
dataOrigin<--method Mass spectrometry data backends
dataOrigin<--method The Spectra class to manage and access MS data
dataStorage-method Mass spectrometry data backends
dataStorage-method The Spectra class to manage and access MS data
dataStorage<--method Mass spectrometry data backends
dropNaSpectraVariables-method Mass spectrometry data backends
dropNaSpectraVariables-method The Spectra class to manage and access MS data

-- E --

executeProcessingStep Processing step
export-method Mass spectrometry data backends
export-method The Spectra class to manage and access MS data

-- F --

filterAcquisitionNum-method Mass spectrometry data backends
filterAcquisitionNum-method The Spectra class to manage and access MS data
filterDataOrigin-method Mass spectrometry data backends
filterDataOrigin-method The Spectra class to manage and access MS data
filterDataStorage-method Mass spectrometry data backends
filterDataStorage-method The Spectra class to manage and access MS data
filterEmptySpectra-method Mass spectrometry data backends
filterEmptySpectra-method The Spectra class to manage and access MS data
filterIntensity-method The Spectra class to manage and access MS data
filterIsolationWindow-method Mass spectrometry data backends
filterIsolationWindow-method The Spectra class to manage and access MS data
filterMsLevel-method Mass spectrometry data backends
filterMsLevel-method The Spectra class to manage and access MS data
filterMzRange-method The Spectra class to manage and access MS data
filterMzValues-method The Spectra class to manage and access MS data
filterPolarity-method Mass spectrometry data backends
filterPolarity-method The Spectra class to manage and access MS data
filterPrecursorMz-method Mass spectrometry data backends
filterPrecursorMz-method The Spectra class to manage and access MS data
filterPrecursorScan-method Mass spectrometry data backends
filterPrecursorScan-method The Spectra class to manage and access MS data
filterRt-method Mass spectrometry data backends
filterRt-method The Spectra class to manage and access MS data

-- I --

intensity-method Mass spectrometry data backends
intensity-method The Spectra class to manage and access MS data
intensity<--method Mass spectrometry data backends
ionCount-method Mass spectrometry data backends
ionCount-method The Spectra class to manage and access MS data
isCentroided-method Mass spectrometry data backends
isCentroided-method The Spectra class to manage and access MS data
isEmpty-method Mass spectrometry data backends
isEmpty-method The Spectra class to manage and access MS data
isolationWindowLowerMz-method Mass spectrometry data backends
isolationWindowLowerMz-method The Spectra class to manage and access MS data
isolationWindowLowerMz<--method Mass spectrometry data backends
isolationWindowLowerMz<--method The Spectra class to manage and access MS data
isolationWindowTargetMz-method Mass spectrometry data backends
isolationWindowTargetMz-method The Spectra class to manage and access MS data
isolationWindowTargetMz<--method Mass spectrometry data backends
isolationWindowTargetMz<--method The Spectra class to manage and access MS data
isolationWindowUpperMz-method Mass spectrometry data backends
isolationWindowUpperMz-method The Spectra class to manage and access MS data
isolationWindowUpperMz<--method Mass spectrometry data backends
isolationWindowUpperMz<--method The Spectra class to manage and access MS data
isReadOnly-method Mass spectrometry data backends

-- J --

joinPeaks Join (map) peaks of two spectra

-- L --

length-method Mass spectrometry data backends
length-method The Spectra class to manage and access MS data
lengths-method Mass spectrometry data backends
lengths-method The Spectra class to manage and access MS data

-- M --

MsBackend Mass spectrometry data backends
MsBackend-class Mass spectrometry data backends
MsBackendDataFrame Mass spectrometry data backends
MsBackendDataFrame-class Mass spectrometry data backends
MsBackendHdf5Peaks Mass spectrometry data backends
MsBackendMzR Mass spectrometry data backends
MsBackendMzR-class Mass spectrometry data backends
msLevel-method Mass spectrometry data backends
msLevel-method The Spectra class to manage and access MS data
mz-method Mass spectrometry data backends
mz-method The Spectra class to manage and access MS data
mz<--method Mass spectrometry data backends

-- P --

peaksData-method Mass spectrometry data backends
peaksData-method The Spectra class to manage and access MS data
peaksData<--method Mass spectrometry data backends
pickPeaks-method The Spectra class to manage and access MS data
plotSpectra Plotting Spectra
plotSpectraMirror Plotting Spectra
plotSpectraOverlay Plotting Spectra
polarity-method Mass spectrometry data backends
polarity-method The Spectra class to manage and access MS data
polarity<--method Mass spectrometry data backends
polarity<--method The Spectra class to manage and access MS data
precScanNum-method Mass spectrometry data backends
precScanNum-method The Spectra class to manage and access MS data
precursorCharge-method Mass spectrometry data backends
precursorCharge-method The Spectra class to manage and access MS data
precursorIntensity-method Mass spectrometry data backends
precursorIntensity-method The Spectra class to manage and access MS data
precursorMz-method Mass spectrometry data backends
precursorMz-method The Spectra class to manage and access MS data
ProcessingStep Processing step

-- R --

replaceIntensitiesBelow-method The Spectra class to manage and access MS data
reset-method Mass spectrometry data backends
reset-method The Spectra class to manage and access MS data
rtime-method Mass spectrometry data backends
rtime-method The Spectra class to manage and access MS data
rtime<--method Mass spectrometry data backends
rtime<--method The Spectra class to manage and access MS data

-- S --

scanIndex-method Mass spectrometry data backends
scanIndex-method The Spectra class to manage and access MS data
selectSpectraVariables-method Mass spectrometry data backends
selectSpectraVariables-method The Spectra class to manage and access MS data
setBackend-method The Spectra class to manage and access MS data
smooth-method The Spectra class to manage and access MS data
smoothed-method Mass spectrometry data backends
smoothed-method The Spectra class to manage and access MS data
smoothed<--method Mass spectrometry data backends
smoothed<--method The Spectra class to manage and access MS data
Spectra The Spectra class to manage and access MS data
Spectra-class The Spectra class to manage and access MS data
Spectra-method The Spectra class to manage and access MS data
spectra-plotting Plotting Spectra
spectraData-method Mass spectrometry data backends
spectraData-method The Spectra class to manage and access MS data
spectraData<--method Mass spectrometry data backends
spectraData<--method The Spectra class to manage and access MS data
spectraNames-method Mass spectrometry data backends
spectraNames-method The Spectra class to manage and access MS data
spectraNames<--method Mass spectrometry data backends
spectraNames<--method The Spectra class to manage and access MS data
spectrapply-method The Spectra class to manage and access MS data
spectraVariables-method Mass spectrometry data backends
spectraVariables-method The Spectra class to manage and access MS data
split-method Mass spectrometry data backends
split-method The Spectra class to manage and access MS data

-- T --

tic-method Mass spectrometry data backends
tic-method The Spectra class to manage and access MS data

-- misc --

$-method Mass spectrometry data backends
$-method The Spectra class to manage and access MS data
$<--method Mass spectrometry data backends
$<--method The Spectra class to manage and access MS data
[-method Mass spectrometry data backends
[-method The Spectra class to manage and access MS data