Spectra Infrastructure for Mass Spectrometry Data

Documentation for package ‘Spectra’ version 1.10.3

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-- A --

acquisitionNum-method	Mass spectrometry data backends
acquisitionNum-method	Base MsBackend class providing data caching mechanism
acquisitionNum-method	The Spectra class to manage and access MS data
addProcessing-method	The Spectra class to manage and access MS data
applyProcessing	The Spectra class to manage and access MS data

-- B --

backendBpparam	Mass spectrometry data backends
backendBpparam-method	Mass spectrometry data backends
backendBpparam-method	The Spectra class to manage and access MS data
backendInitialize	Mass spectrometry data backends
backendInitialize-method	Mass spectrometry data backends
backendInitialize-method	Base MsBackend class providing data caching mechanism
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	Base MsBackend class providing data caching mechanism
centroided-method	The Spectra class to manage and access MS data
centroided<--method	Mass spectrometry data backends
centroided<--method	Base MsBackend class providing data caching mechanism
centroided<--method	The Spectra class to manage and access MS data
chunkapply	Apply a function stepwise to chunks of data
class:MsBackend	Mass spectrometry data backends
collisionEnergy-method	Mass spectrometry data backends
collisionEnergy-method	Base MsBackend class providing data caching mechanism
collisionEnergy-method	The Spectra class to manage and access MS data
collisionEnergy<--method	Mass spectrometry data backends
collisionEnergy<--method	Base MsBackend class providing data caching mechanism
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
computeMzDeltas	MZ delta Quality Control
concatenateSpectra	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
coreSpectraVariables	The Spectra class to manage and access MS data
countIdentifications	Count the number of identifications per scan

-- D --

dataOrigin-method	Mass spectrometry data backends
dataOrigin-method	Base MsBackend class providing data caching mechanism
dataOrigin-method	The Spectra class to manage and access MS data
dataOrigin<--method	Mass spectrometry data backends
dataOrigin<--method	Base MsBackend class providing data caching mechanism
dataOrigin<--method	The Spectra class to manage and access MS data
dataStorage-method	Mass spectrometry data backends
dataStorage-method	Base MsBackend class providing data caching mechanism
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 --

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

-- F --

fft_spectrum	Fast fourier transform artefact filter
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
filterFourierTransformArtefacts	Fast fourier transform artefact filter
filterFourierTransformArtefacts-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
filterPrecursorCharge-method	Mass spectrometry data backends
filterPrecursorCharge-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
filterPrecursorMzRange-method	Mass spectrometry data backends
filterPrecursorMzRange-method	The Spectra class to manage and access MS data
filterPrecursorMzValues-method	Mass spectrometry data backends
filterPrecursorMzValues-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	Base MsBackend class providing data caching mechanism
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	Base MsBackend class providing data caching mechanism
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	Base MsBackend class providing data caching mechanism
isEmpty-method	The Spectra class to manage and access MS data
isolationWindowLowerMz-method	Mass spectrometry data backends
isolationWindowLowerMz-method	Base MsBackend class providing data caching mechanism
isolationWindowLowerMz-method	The Spectra class to manage and access MS data
isolationWindowLowerMz<--method	Mass spectrometry data backends
isolationWindowLowerMz<--method	Base MsBackend class providing data caching mechanism
isolationWindowLowerMz<--method	The Spectra class to manage and access MS data
isolationWindowTargetMz-method	Mass spectrometry data backends
isolationWindowTargetMz-method	Base MsBackend class providing data caching mechanism
isolationWindowTargetMz-method	The Spectra class to manage and access MS data
isolationWindowTargetMz<--method	Mass spectrometry data backends
isolationWindowTargetMz<--method	Base MsBackend class providing data caching mechanism
isolationWindowTargetMz<--method	The Spectra class to manage and access MS data
isolationWindowUpperMz-method	Mass spectrometry data backends
isolationWindowUpperMz-method	Base MsBackend class providing data caching mechanism
isolationWindowUpperMz-method	The Spectra class to manage and access MS data
isolationWindowUpperMz<--method	Mass spectrometry data backends
isolationWindowUpperMz<--method	Base MsBackend class providing data caching mechanism
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
joinPeaksGnps	Join (map) peaks of two spectra
joinSpectraData	The Spectra class to manage and access MS data

-- L --

length-method	Mass spectrometry data backends
length-method	Base MsBackend class providing data caching mechanism
length-method	The Spectra class to manage and access MS data
lengths-method	Mass spectrometry data backends
lengths-method	Base MsBackend class providing data caching mechanism
lengths-method	The Spectra class to manage and access MS data

-- M --

MsBackend	Mass spectrometry data backends
MsBackend-class	Mass spectrometry data backends
MsBackendCached	Base MsBackend class providing data caching mechanism
MsBackendCached-class	Base MsBackend class providing data caching mechanism
MsBackendDataFrame	Mass spectrometry data backends
MsBackendDataFrame-class	Mass spectrometry data backends
MsBackendHdf5Peaks	Mass spectrometry data backends
MsBackendMemory	Mass spectrometry data backends
MsBackendMemory-class	Mass spectrometry data backends
MsBackendMzR	Mass spectrometry data backends
MsBackendMzR-class	Mass spectrometry data backends
msLevel-method	Mass spectrometry data backends
msLevel-method	Base MsBackend class providing data caching mechanism
msLevel-method	The Spectra class to manage and access MS data
mz-method	Mass spectrometry data backends
mz-method	Base MsBackend class providing data caching mechanism
mz-method	The Spectra class to manage and access MS data
mz<--method	Mass spectrometry data backends

-- N --

neutralLoss	Calculate Neutral Loss Spectra
neutralLoss-method	Calculate Neutral Loss Spectra

-- P --

peaksData-method	Mass spectrometry data backends
peaksData-method	The Spectra class to manage and access MS data
peaksData<--method	Mass spectrometry data backends
peaksVariables-method	Mass spectrometry data backends
peaksVariables-method	The Spectra class to manage and access MS data
pickPeaks-method	The Spectra class to manage and access MS data
plotMzDelta	MZ delta Quality Control
plotSpectra	Plotting Spectra
plotSpectraMirror	Plotting Spectra
plotSpectraMirror-method	Plotting Spectra
plotSpectraOverlay	Plotting Spectra
polarity-method	Mass spectrometry data backends
polarity-method	Base MsBackend class providing data caching mechanism
polarity-method	The Spectra class to manage and access MS data
polarity<--method	Mass spectrometry data backends
polarity<--method	Base MsBackend class providing data caching mechanism
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	Base MsBackend class providing data caching mechanism
precursorCharge-method	The Spectra class to manage and access MS data
precursorIntensity-method	Mass spectrometry data backends
precursorIntensity-method	Base MsBackend class providing data caching mechanism
precursorIntensity-method	The Spectra class to manage and access MS data
precursorMz-method	Mass spectrometry data backends
precursorMz-method	Base MsBackend class providing data caching mechanism
precursorMz-method	The Spectra class to manage and access MS data
PrecursorMzParam	Calculate Neutral Loss Spectra
processingLog	The Spectra class to manage and access MS data

-- 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	Base MsBackend class providing data caching mechanism
rtime-method	The Spectra class to manage and access MS data
rtime<--method	Mass spectrometry data backends
rtime<--method	Base MsBackend class providing data caching mechanism
rtime<--method	The Spectra class to manage and access MS data

-- S --

scanIndex-method	Mass spectrometry data backends
scanIndex-method	Base MsBackend class providing data caching mechanism
scanIndex-method	The Spectra class to manage and access MS data
selectSpectraVariables-method	Mass spectrometry data backends
selectSpectraVariables-method	Base MsBackend class providing data caching mechanism
selectSpectraVariables-method	The Spectra class to manage and access MS data
setBackend-method	The Spectra class to manage and access MS data
show-method	Base MsBackend class providing data caching mechanism
smooth-method	The Spectra class to manage and access MS data
smoothed-method	Mass spectrometry data backends
smoothed-method	Base MsBackend class providing data caching mechanism
smoothed-method	The Spectra class to manage and access MS data
smoothed<--method	Mass spectrometry data backends
smoothed<--method	Base MsBackend class providing data caching mechanism
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	Base MsBackend class providing data caching mechanism
spectraData-method	The Spectra class to manage and access MS data
spectraData<--method	Mass spectrometry data backends
spectraData<--method	Base MsBackend class providing data caching mechanism
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
spectraVariableMapping	Mapping between spectra variables and data file fields
spectraVariables-method	Mass spectrometry data backends
spectraVariables-method	Base MsBackend class providing data caching mechanism
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
supportsSetBackend	Mass spectrometry data backends
supportsSetBackend-method	Mass spectrometry data backends

-- T --

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

-- U --

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

-- misc --

$-method	Mass spectrometry data backends
$-method	Base MsBackend class providing data caching mechanism
$-method	The Spectra class to manage and access MS data
$<--method	Mass spectrometry data backends
$<--method	Base MsBackend class providing data caching mechanism
$<--method	The Spectra class to manage and access MS data
[-method	Mass spectrometry data backends
[-method	Base MsBackend class providing data caching mechanism
[-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