Spectra Infrastructure for Mass Spectrometry Data

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Documentation for package ‘Spectra’ version 1.18.2

• 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	Base MsBackend class providing data caching mechanism
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