# Spectra Infrastructure for Mass Spectrometry Data

## Documentation for package ‘Spectra’ version 1.19.0

- 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 | Accessing mass spectrometry data
acquisitionNum-method | Mass spectrometry data backends
acquisitionNum-method | Base MsBackend class providing data caching mechanism
acquisitionNum-method | Accessing mass spectrometry data
addProcessing | Data manipulation and analysis methods
addProcessing-method | Data manipulation and analysis methods
applyProcessing | Data manipulation and analysis methods
applyProcessing-method | Data manipulation and analysis methods
asDataFrame | Accessing mass spectrometry data

## -- B --

backendBpparam | Mass spectrometry data backends
backendBpparam-method | Mass spectrometry data backends
backendBpparam-method | Parallel and chunk-wise processing of 'Spectra'
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 | Mass spectrometry data backends
backendParallelFactor-method | Mass spectrometry data backends
backendRequiredSpectraVariables | Mass spectrometry data backends
backendRequiredSpectraVariables-method | Mass spectrometry data backends
bin | Data manipulation and analysis methods
bin-method | Data manipulation and analysis methods

## -- C --

c-method | Merging, aggregating and splitting Spectra
cbind2 | Merging, aggregating and splitting Spectra
cbind2-method | Mass spectrometry data backends
cbind2-method | Merging, aggregating and splitting Spectra
centroided | Accessing mass spectrometry data
centroided-method | Mass spectrometry data backends
centroided-method | Base MsBackend class providing data caching mechanism
centroided-method | Accessing mass spectrometry data
centroided<--method | Mass spectrometry data backends
centroided<--method | Base MsBackend class providing data caching mechanism
centroided<--method | Accessing mass spectrometry data
chunkapply | Apply a function stepwise to chunks of data
class:MsBackend | Mass spectrometry data backends
collisionEnergy | Accessing mass spectrometry data
collisionEnergy-method | Mass spectrometry data backends
collisionEnergy-method | Base MsBackend class providing data caching mechanism
collisionEnergy-method | Accessing mass spectrometry data
collisionEnergy<--method | Mass spectrometry data backends
collisionEnergy<--method | Base MsBackend class providing data caching mechanism
collisionEnergy<--method | Accessing mass spectrometry data
combinePeaks | Aggregating and combining mass peaks data
combinePeaks-method | Aggregating and combining mass peaks data
combinePeaksData | Combine peaks with similar m/z across spectra
combineSpectra | Merging, aggregating and splitting Spectra
compareSpectra | Spectra similarity calculations
compareSpectra-method | Spectra similarity calculations
computeMzDeltas | MZ delta Quality Control
concatenateSpectra | Merging, aggregating and splitting Spectra
containsMz | Data manipulation and analysis methods
containsMz-method | Data manipulation and analysis methods
containsNeutralLoss | Data manipulation and analysis methods
containsNeutralLoss-method | Data manipulation and analysis methods
coreSpectraVariables | Accessing mass spectrometry data
countIdentifications | Count the number of identifications per scan

## -- D --

dataOrigin | Accessing mass spectrometry data
dataOrigin-method | Mass spectrometry data backends
dataOrigin-method | Base MsBackend class providing data caching mechanism
dataOrigin-method | Accessing mass spectrometry data
dataOrigin<--method | Mass spectrometry data backends
dataOrigin<--method | Base MsBackend class providing data caching mechanism
dataOrigin<--method | Accessing mass spectrometry data
dataStorage | Accessing mass spectrometry data
dataStorage-method | Mass spectrometry data backends
dataStorage-method | Base MsBackend class providing data caching mechanism
dataStorage-method | Accessing mass spectrometry data
dataStorage<--method | Mass spectrometry data backends
dataStorageBasePath | Mass spectrometry data backends
dataStorageBasePath-method | Mass spectrometry data backends
dataStorageBasePath-method | The Spectra class to manage and access MS data
dataStorageBasePath<- | Mass spectrometry data backends
dataStorageBasePath<--method | Mass spectrometry data backends
dataStorageBasePath<--method | The Spectra class to manage and access MS data
deisotopeSpectra | Filter and subset Spectra objects
dropNaSpectraVariables | Filter and subset Spectra objects
dropNaSpectraVariables-method | Mass spectrometry data backends
dropNaSpectraVariables-method | Filter and subset Spectra objects

## -- E --

entropy | Data manipulation and analysis methods
entropy-method | Data manipulation and analysis methods
estimatePrecursorIntensity | Estimate Precursor Intensities
estimatePrecursorIntensity-method | Estimate Precursor Intensities
estimatePrecursorMz | Estimating precursor m/z valus for DDA data
export | 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
extractByIndex | Mass spectrometry data backends
extractByIndex-method | Mass spectrometry data backends
extractByIndex-method | Base MsBackend class providing data caching mechanism

## -- F --

fft_spectrum | Fast fourier transform artefact filter
fillCoreSpectraVariables | Fill spectra data with columns for missing core variables
filterAcquisitionNum | Filter and subset Spectra objects
filterAcquisitionNum-method | Mass spectrometry data backends
filterAcquisitionNum-method | Filter and subset Spectra objects
filterDataOrigin | Filter and subset Spectra objects
filterDataOrigin-method | Mass spectrometry data backends
filterDataOrigin-method | Filter and subset Spectra objects
filterDataStorage | Filter and subset Spectra objects
filterDataStorage-method | Mass spectrometry data backends
filterDataStorage-method | Filter and subset Spectra objects
filterEmptySpectra | Filter and subset Spectra objects
filterEmptySpectra-method | Mass spectrometry data backends
filterEmptySpectra-method | Filter and subset Spectra objects
filterFourierTransformArtefacts | Fast fourier transform artefact filter
filterFourierTransformArtefacts-method | Filter and subset Spectra objects
filterIntensity | Filter and subset Spectra objects
filterIntensity-method | Filter and subset Spectra objects
filterIsolationWindow | Filter and subset Spectra objects
filterIsolationWindow-method | Mass spectrometry data backends
filterIsolationWindow-method | Filter and subset Spectra objects
filterMsLevel | Filter and subset Spectra objects
filterMsLevel-method | Mass spectrometry data backends
filterMsLevel-method | Filter and subset Spectra objects
filterMzRange | Filter and subset Spectra objects
filterMzRange-method | Filter and subset Spectra objects
filterMzValues | Filter and subset Spectra objects
filterMzValues-method | Filter and subset Spectra objects
filterPeaksRanges | Filter peaks based on spectra and peaks variable ranges
filterPolarity | Filter and subset Spectra objects
filterPolarity-method | Mass spectrometry data backends
filterPolarity-method | Filter and subset Spectra objects
filterPrecursorCharge | Filter and subset Spectra objects
filterPrecursorCharge-method | Mass spectrometry data backends
filterPrecursorCharge-method | Filter and subset Spectra objects
filterPrecursorIsotopes | Filter and subset Spectra objects
filterPrecursorMaxIntensity | Filter and subset Spectra objects
filterPrecursorMz-method | Mass spectrometry data backends
filterPrecursorMz-method | Filter and subset Spectra objects
filterPrecursorMzRange | Filter and subset Spectra objects
filterPrecursorMzRange-method | Mass spectrometry data backends
filterPrecursorMzRange-method | Filter and subset Spectra objects
filterPrecursorMzValues | Filter and subset Spectra objects
filterPrecursorMzValues-method | Mass spectrometry data backends
filterPrecursorMzValues-method | Filter and subset Spectra objects
filterPrecursorPeaks | Filter and subset Spectra objects
filterPrecursorScan | Filter and subset Spectra objects
filterPrecursorScan-method | Mass spectrometry data backends
filterPrecursorScan-method | Filter and subset Spectra objects
filterRanges | Filter and subset Spectra objects
filterRanges-method | Mass spectrometry data backends
filterRanges-method | Filter and subset Spectra objects
filterRt | Filter and subset Spectra objects
filterRt-method | Mass spectrometry data backends
filterRt-method | Filter and subset Spectra objects
filterValues | Filter and subset Spectra objects
filterValues-method | Mass spectrometry data backends
filterValues-method | Filter and subset Spectra objects

## -- I --

intensity | Accessing mass spectrometry data
intensity-method | Mass spectrometry data backends
intensity-method | Base MsBackend class providing data caching mechanism
intensity-method | Accessing mass spectrometry data
intensity<--method | Mass spectrometry data backends
ionCount | Accessing mass spectrometry data
ionCount-method | Mass spectrometry data backends
ionCount-method | Base MsBackend class providing data caching mechanism
ionCount-method | Accessing mass spectrometry data
isCentroided | Accessing mass spectrometry data
isCentroided-method | Mass spectrometry data backends
isCentroided-method | Accessing mass spectrometry data
isEmpty | Accessing mass spectrometry data
isEmpty-method | Mass spectrometry data backends
isEmpty-method | Base MsBackend class providing data caching mechanism
isEmpty-method | Accessing mass spectrometry data
isolationWindowLowerMz | Accessing mass spectrometry data
isolationWindowLowerMz-method | Mass spectrometry data backends
isolationWindowLowerMz-method | Base MsBackend class providing data caching mechanism
isolationWindowLowerMz-method | Accessing mass spectrometry data
isolationWindowLowerMz<--method | Mass spectrometry data backends
isolationWindowLowerMz<--method | Base MsBackend class providing data caching mechanism
isolationWindowLowerMz<--method | Accessing mass spectrometry data
isolationWindowTargetMz | Accessing mass spectrometry data
isolationWindowTargetMz-method | Mass spectrometry data backends
isolationWindowTargetMz-method | Base MsBackend class providing data caching mechanism
isolationWindowTargetMz-method | Accessing mass spectrometry data
isolationWindowTargetMz<--method | Mass spectrometry data backends
isolationWindowTargetMz<--method | Base MsBackend class providing data caching mechanism
isolationWindowTargetMz<--method | Accessing mass spectrometry data
isolationWindowUpperMz | Accessing mass spectrometry data
isolationWindowUpperMz-method | Mass spectrometry data backends
isolationWindowUpperMz-method | Base MsBackend class providing data caching mechanism
isolationWindowUpperMz-method | Accessing mass spectrometry data
isolationWindowUpperMz<--method | Mass spectrometry data backends
isolationWindowUpperMz<--method | Base MsBackend class providing data caching mechanism
isolationWindowUpperMz<--method | Accessing mass spectrometry 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 | Merging, aggregating and splitting Spectra

## -- L --

length-method | Mass spectrometry data backends
length-method | Base MsBackend class providing data caching mechanism
length-method | Accessing mass spectrometry data
lengths | Accessing mass spectrometry data
lengths-method | Mass spectrometry data backends
lengths-method | Base MsBackend class providing data caching mechanism
lengths-method | Accessing mass spectrometry 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 | Accessing mass spectrometry data
msLevel-method | Mass spectrometry data backends
msLevel-method | Base MsBackend class providing data caching mechanism
msLevel-method | Accessing mass spectrometry data
msLeveL<--method | Mass spectrometry data backends
msLevel<--method | Mass spectrometry data backends
mz | Accessing mass spectrometry data
mz-method | Mass spectrometry data backends
mz-method | Base MsBackend class providing data caching mechanism
mz-method | Accessing mass spectrometry data
mz<--method | Mass spectrometry data backends

## -- N --

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

## -- P --

peaksData | Accessing mass spectrometry data
peaksData-method | Mass spectrometry data backends
peaksData-method | Accessing mass spectrometry data
peaksData<--method | Mass spectrometry data backends
peaksVariables | Accessing mass spectrometry data
peaksVariables-method | Mass spectrometry data backends
peaksVariables-method | Accessing mass spectrometry data
pickPeaks | Data manipulation and analysis methods
pickPeaks-method | Data manipulation and analysis methods
plotMzDelta | MZ delta Quality Control
plotSpectra | Plotting Spectra
plotSpectraMirror | Plotting Spectra
plotSpectraMirror-method | Plotting Spectra
plotSpectraOverlay | Plotting Spectra
polarity | Accessing mass spectrometry data
polarity-method | Mass spectrometry data backends
polarity-method | Base MsBackend class providing data caching mechanism
polarity-method | Accessing mass spectrometry data
polarity<--method | Mass spectrometry data backends
polarity<--method | Base MsBackend class providing data caching mechanism
polarity<--method | Accessing mass spectrometry data
precScanNum-method | Mass spectrometry data backends
precScanNum-method | Accessing mass spectrometry data
precursorCharge | Accessing mass spectrometry data
precursorCharge-method | Mass spectrometry data backends
precursorCharge-method | Base MsBackend class providing data caching mechanism
precursorCharge-method | Accessing mass spectrometry data
precursorIntensity | Accessing mass spectrometry data
precursorIntensity-method | Mass spectrometry data backends
precursorIntensity-method | Base MsBackend class providing data caching mechanism
precursorIntensity-method | Accessing mass spectrometry data
precursorMz | Accessing mass spectrometry data
precursorMz-method | Mass spectrometry data backends
precursorMz-method | Base MsBackend class providing data caching mechanism
precursorMz-method | Accessing mass spectrometry data
precursorMz<--method | Mass spectrometry data backends
precursorMz<--method | Accessing mass spectrometry data
PrecursorMzParam | Calculate Neutral Loss Spectra
processingChunkFactor | Parallel and chunk-wise processing of 'Spectra'
processingChunkFactor-method | Parallel and chunk-wise processing of 'Spectra'
processingChunkSize | Parallel and chunk-wise processing of 'Spectra'
processingChunkSize-method | Parallel and chunk-wise processing of 'Spectra'
processingChunkSize<- | Parallel and chunk-wise processing of 'Spectra'
processingChunkSize<--method | Parallel and chunk-wise processing of 'Spectra'
processingLog | Data manipulation and analysis methods

## -- R --

reduceSpectra | Filter and subset Spectra objects
replaceIntensitiesBelow | Data manipulation and analysis methods
replaceIntensitiesBelow-method | Data manipulation and analysis methods
reset | Data manipulation and analysis methods
reset-method | Mass spectrometry data backends
reset-method | Data manipulation and analysis methods
rtime | Accessing mass spectrometry data
rtime-method | Mass spectrometry data backends
rtime-method | Base MsBackend class providing data caching mechanism
rtime-method | Accessing mass spectrometry data
rtime<--method | Mass spectrometry data backends
rtime<--method | Base MsBackend class providing data caching mechanism
rtime<--method | Accessing mass spectrometry data

## -- S --

scalePeaks | Data manipulation and analysis methods
scanIndex | Accessing mass spectrometry data
scanIndex-method | Mass spectrometry data backends
scanIndex-method | Base MsBackend class providing data caching mechanism
scanIndex-method | Accessing mass spectrometry data
selectSpectraVariables | Filter and subset Spectra objects
selectSpectraVariables-method | Mass spectrometry data backends
selectSpectraVariables-method | Base MsBackend class providing data caching mechanism
selectSpectraVariables-method | Filter and subset Spectra objects
setBackend | 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 | Data manipulation and analysis methods
smooth-method | Data manipulation and analysis methods
smoothed | Accessing mass spectrometry data
smoothed-method | Mass spectrometry data backends
smoothed-method | Base MsBackend class providing data caching mechanism
smoothed-method | Accessing mass spectrometry data
smoothed<--method | Mass spectrometry data backends
smoothed<--method | Base MsBackend class providing data caching mechanism
smoothed<--method | Accessing mass spectrometry 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 | Accessing mass spectrometry data
spectraData-method | Mass spectrometry data backends
spectraData-method | Base MsBackend class providing data caching mechanism
spectraData-method | Accessing mass spectrometry data
spectraData<--method | Mass spectrometry data backends
spectraData<--method | Base MsBackend class providing data caching mechanism
spectraData<--method | Accessing mass spectrometry data
spectraNames | Accessing mass spectrometry data
spectraNames-method | Mass spectrometry data backends
spectraNames-method | Accessing mass spectrometry data
spectraNames<--method | Mass spectrometry data backends
spectraNames<--method | Accessing mass spectrometry data
spectrapply | Data manipulation and analysis methods
spectrapply-method | Data manipulation and analysis methods
spectraVariableMapping | Mapping between spectra variables and data file fields
spectraVariableMapping<- | Mapping between spectra variables and data file fields
spectraVariables | Accessing mass spectrometry data
spectraVariables-method | Mass spectrometry data backends
spectraVariables-method | Base MsBackend class providing data caching mechanism
spectraVariables-method | Accessing mass spectrometry data
split | Merging, aggregating and splitting Spectra
split-method | Mass spectrometry data backends
split-method | Merging, aggregating and splitting Spectra
supportsSetBackend | Mass spectrometry data backends
supportsSetBackend-method | Mass spectrometry data backends

## -- T --

tic | Accessing mass spectrometry data
tic-method | Mass spectrometry data backends
tic-method | Accessing mass spectrometry data

## -- U --

uniqueMsLevels | Accessing mass spectrometry data
uniqueMsLevels-method | Mass spectrometry data backends
uniqueMsLevels-method | Accessing mass spectrometry data

## -- misc --

$-method | Mass spectrometry data backends
$-method | Base MsBackend class providing data caching mechanism
$-method | Accessing mass spectrometry data
$<--method | Mass spectrometry data backends
$<--method | Base MsBackend class providing data caching mechanism
$<--method | Accessing mass spectrometry data
[-method | Mass spectrometry data backends
[-method | Base MsBackend class providing data caching mechanism
[-method | Filter and subset Spectra objects
[[-method | Mass spectrometry data backends
[[-method | Accessing mass spectrometry data
[[<--method | Mass spectrometry data backends
[[<--method | Accessing mass spectrometry data