# Spectra Infrastructure for Mass Spectrometry Data

## Documentation for package ‘Spectra’ version 1.4.3

- DESCRIPTION file.
- User guides, package vignettes and other documentation.

## Help Pages

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-method | 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
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

## -- 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 --

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 --

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
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
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
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 | 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
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 | 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
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 | 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
[[-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