Package index

All functions

backendBpparam(<MsBackend>) backendInitialize(<MsBackend>) backendMerge(<list>) backendMerge(<MsBackend>) backendParallelFactor(<MsBackend>) export(<MsBackend>) acquisitionNum(<MsBackend>) peaksData(<MsBackend>) peaksVariables(<MsBackend>) centroided(<MsBackend>) `centroided<-`(<MsBackend>) collisionEnergy(<MsBackend>) `collisionEnergy<-`(<MsBackend>) dataOrigin(<MsBackend>) `dataOrigin<-`(<MsBackend>) dataStorage(<MsBackend>) `dataStorage<-`(<MsBackend>) dropNaSpectraVariables(<MsBackend>) filterAcquisitionNum(<MsBackend>) filterDataOrigin(<MsBackend>) filterDataStorage(<MsBackend>) filterEmptySpectra(<MsBackend>) filterIsolationWindow(<MsBackend>) filterMsLevel(<MsBackend>) filterPolarity(<MsBackend>) filterPrecursorMzRange(<MsBackend>) filterPrecursorMz(<MsBackend>) filterPrecursorMzValues(<MsBackend>) filterPrecursorCharge(<MsBackend>) filterPrecursorScan(<MsBackend>) filterRanges(<MsBackend>) filterRt(<MsBackend>) filterValues(<MsBackend>) intensity(<MsBackend>) `intensity<-`(<MsBackend>) ionCount(<MsBackend>) isCentroided(<MsBackend>) isEmpty(<MsBackend>) isolationWindowLowerMz(<MsBackend>) `isolationWindowLowerMz<-`(<MsBackend>) isolationWindowTargetMz(<MsBackend>) `isolationWindowTargetMz<-`(<MsBackend>) isolationWindowUpperMz(<MsBackend>) `isolationWindowUpperMz<-`(<MsBackend>) isReadOnly(<MsBackend>) length(<MsBackend>) msLevel(<MsBackend>) mz(<MsBackend>) `mz<-`(<MsBackend>) lengths(<MsBackend>) polarity(<MsBackend>) `polarity<-`(<MsBackend>) precScanNum(<MsBackend>) precursorCharge(<MsBackend>) precursorIntensity(<MsBackend>) precursorMz(<MsBackend>) `peaksData<-`(<MsBackend>) reset(<MsBackend>) rtime(<MsBackend>) `rtime<-`(<MsBackend>) scanIndex(<MsBackend>) selectSpectraVariables(<MsBackend>) smoothed(<MsBackend>) `smoothed<-`(<MsBackend>) spectraData(<MsBackend>) `spectraData<-`(<MsBackend>) spectraNames(<MsBackend>) `spectraNames<-`(<MsBackend>) spectraVariables(<MsBackend>) split(<MsBackend>,<ANY>) supportsSetBackend(<MsBackend>) tic(<MsBackend>) `[`(<MsBackend>) `$`(<MsBackend>) `$<-`(<MsBackend>) `[[`(<MsBackend>) `[[<-`(<MsBackend>) uniqueMsLevels(<MsBackend>) dataStorageBasePath(<MsBackend>) `dataStorageBasePath<-`(<MsBackend>) MsBackendDataFrame() backendInitialize(<MsBackendDataFrame>) MsBackendHdf5Peaks() MsBackendMemory() backendInitialize(<MsBackendMemory>) MsBackendMzR()

Mass spectrometry data backends

MsBackendCached() backendInitialize(<MsBackendCached>) dataStorage(<MsBackendCached>) length(<MsBackendCached>) spectraVariables(<MsBackendCached>) spectraData(<MsBackendCached>) `spectraData<-`(<MsBackendCached>) `[`(<MsBackendCached>) `$`(<MsBackendCached>) `$<-`(<MsBackendCached>) selectSpectraVariables(<MsBackendCached>) show(<MsBackendCached>) acquisitionNum(<MsBackendCached>) centroided(<MsBackendCached>) `centroided<-`(<MsBackendCached>) collisionEnergy(<MsBackendCached>) `collisionEnergy<-`(<MsBackendCached>) dataOrigin(<MsBackendCached>) `dataOrigin<-`(<MsBackendCached>) msLevel(<MsBackendCached>) intensity(<MsBackendCached>) ionCount(<MsBackendCached>) isEmpty(<MsBackendCached>) isolationWindowLowerMz(<MsBackendCached>) `isolationWindowLowerMz<-`(<MsBackendCached>) isolationWindowTargetMz(<MsBackendCached>) `isolationWindowTargetMz<-`(<MsBackendCached>) isolationWindowUpperMz(<MsBackendCached>) `isolationWindowUpperMz<-`(<MsBackendCached>) lengths(<MsBackendCached>) mz(<MsBackendCached>) polarity(<MsBackendCached>) `polarity<-`(<MsBackendCached>) precursorCharge(<MsBackendCached>) precursorIntensity(<MsBackendCached>) precursorMz(<MsBackendCached>) rtime(<MsBackendCached>) `rtime<-`(<MsBackendCached>) scanIndex(<MsBackendCached>) smoothed(<MsBackendCached>) `smoothed<-`(<MsBackendCached>)

Base MsBackend class providing data caching mechanism

applyProcessing() concatenateSpectra() combineSpectra() joinSpectraData() processingLog() deisotopeSpectra() reduceSpectra() filterPrecursorMaxIntensity() filterPrecursorIsotopes() scalePeaks() filterPrecursorPeaks() Spectra(<missing>) Spectra(<MsBackend>) Spectra(<character>) Spectra(<ANY>) setBackend(<Spectra>,<MsBackend>) c(<Spectra>) split(<Spectra>,<ANY>) export(<Spectra>) acquisitionNum(<Spectra>) peaksData(<Spectra>) peaksVariables(<Spectra>) centroided(<Spectra>) `centroided<-`(<Spectra>) collisionEnergy(<Spectra>) `collisionEnergy<-`(<Spectra>) dataOrigin(<Spectra>) `dataOrigin<-`(<Spectra>) dataStorage(<Spectra>) dropNaSpectraVariables(<Spectra>) intensity(<Spectra>) ionCount(<Spectra>) isCentroided(<Spectra>) isEmpty(<Spectra>) isolationWindowLowerMz(<Spectra>) `isolationWindowLowerMz<-`(<Spectra>) isolationWindowTargetMz(<Spectra>) `isolationWindowTargetMz<-`(<Spectra>) isolationWindowUpperMz(<Spectra>) `isolationWindowUpperMz<-`(<Spectra>) containsMz(<Spectra>) containsNeutralLoss(<Spectra>) spectrapply(<Spectra>) length(<Spectra>) msLevel(<Spectra>) mz(<Spectra>) lengths(<Spectra>) polarity(<Spectra>) `polarity<-`(<Spectra>) precScanNum(<Spectra>) precursorCharge(<Spectra>) precursorIntensity(<Spectra>) precursorMz(<Spectra>) rtime(<Spectra>) `rtime<-`(<Spectra>) scanIndex(<Spectra>) selectSpectraVariables(<Spectra>) smoothed(<Spectra>) `smoothed<-`(<Spectra>) spectraData(<Spectra>) `spectraData<-`(<Spectra>) spectraNames(<Spectra>) `spectraNames<-`(<Spectra>) spectraVariables(<Spectra>) tic(<Spectra>) `$`(<Spectra>) `$<-`(<Spectra>) `[[`(<Spectra>) `[[<-`(<Spectra>) `[`(<Spectra>) filterAcquisitionNum(<Spectra>) filterEmptySpectra(<Spectra>) filterDataOrigin(<Spectra>) filterDataStorage(<Spectra>) filterFourierTransformArtefacts(<Spectra>) filterIntensity(<Spectra>) filterIsolationWindow(<Spectra>) filterMsLevel(<Spectra>) filterMzRange(<Spectra>) filterMzValues(<Spectra>) filterPolarity(<Spectra>) filterPrecursorMz(<Spectra>) filterPrecursorMzRange(<Spectra>) filterPrecursorMzValues(<Spectra>) filterPrecursorCharge(<Spectra>) filterPrecursorScan(<Spectra>) filterRt(<Spectra>) reset(<Spectra>) filterRanges(<Spectra>) filterValues(<Spectra>) bin(<Spectra>) compareSpectra(<Spectra>,<Spectra>) compareSpectra(<Spectra>,<missing>) pickPeaks(<Spectra>) replaceIntensitiesBelow(<Spectra>) smooth(<Spectra>) addProcessing(<Spectra>) coreSpectraVariables() uniqueMsLevels(<Spectra>) backendBpparam(<Spectra>) combinePeaks(<Spectra>) entropy(<Spectra>) entropy(<ANY>) dataStorageBasePath(<Spectra>) `dataStorageBasePath<-`(<Spectra>) asDataFrame()

The Spectra class to manage and access MS data

chunkapply()

Apply a function stepwise to chunks of data

combinePeaksData()

Combine peaks with similar m/z across spectra

countIdentifications()

Count the number of identifications per scan

estimatePrecursorIntensity(<Spectra>)

Estimate Precursor Intensities

estimatePrecursorMz()

Estimating precursor m/z valus for DDA data

filterFourierTransformArtefacts fft_spectrum

Fast fourier transform artefact filter

filterPeaksRanges()

Filter peaks based on spectra and peaks variable ranges

joinPeaks() joinPeaksGnps() joinPeaksNone()

Join (map) peaks of two spectra

neutralLoss() PrecursorMzParam()

Calculate Neutral Loss Spectra

computeMzDeltas() plotMzDelta()

MZ delta Quality Control

processingChunkSize() `processingChunkSize<-`() processingChunkFactor()

Parallel and chunk-wise processing of Spectra

plotSpectra() plotSpectraOverlay() plotSpectraMirror(<Spectra>)

Plotting Spectra

spectraVariableMapping()

Mapping between spectra variables and data file fields