Spectra Infrastructure for Mass Spectrometry Data

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Documentation for package ‘Spectra’ version 1.14.0

• DESCRIPTION file.
• User guides, package vignettes and other documentation.
• Package NEWS.

Help Pages

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

-- 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
backendParallelFactor-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	The Spectra class to manage and access MS data
combinePeaks-method	The Spectra class to manage and access MS data
combinePeaksData	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
deisotopeSpectra	The Spectra class to manage and access MS data
dropNaSpectraVariables-method	Mass spectrometry data backends
dropNaSpectraVariables-method	The Spectra class to manage and access MS data

-- E --

entropy-method	The Spectra class to manage and access MS data
estimatePrecursorIntensity	Estimate Precursor Intensities
estimatePrecursorMz	Estimating precursor m/z valus for DDA 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
filterPrecursorIsotopes	The Spectra class to manage and access MS data
filterPrecursorMaxIntensity	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
filterPrecursorPeaks	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
filterRanges-method	Mass spectrometry data backends
filterRanges-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
filterValues-method	Mass spectrometry data backends
filterValues-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
joinPeaksNone	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
processingChunkFactor	Parallel and chunk-wise processing of 'Spectra'
processingChunkSize	Parallel and chunk-wise processing of 'Spectra'
processingChunkSize<-	Parallel and chunk-wise processing of 'Spectra'
processingLog	The Spectra class to manage and access MS data

-- R --

reduceSpectra	The Spectra class to manage and access MS data
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 --

scalePeaks	The Spectra class to manage and access MS data
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