Package index

All functions

backendBpparam(<MsBackend>) backendInitialize(<MsBackend>) backendMerge(<list>) backendMerge(<MsBackend>) backendParallelFactor(<MsBackend>) export(<MsBackend>) acquisitionNum(<MsBackend>) peaksData(<MsBackend>) peaksVariables(<MsBackend>) cbind2(<MsBackend>,<dataframeOrDataFrameOrmatrix>) centroided(<MsBackend>) `centroided<-`(<MsBackend>) collisionEnergy(<MsBackend>) `collisionEnergy<-`(<MsBackend>) dataOrigin(<MsBackend>) `dataOrigin<-`(<MsBackend>) dataStorage(<MsBackend>) `dataStorage<-`(<MsBackend>) dropNaSpectraVariables(<MsBackend>) extractByIndex(<MsBackend>,<ANY>) extractByIndex(<MsBackend>,<missing>) 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>) `msLevel<-`(<MsBackend>) mz(<MsBackend>) `mz<-`(<MsBackend>) lengths(<MsBackend>) polarity(<MsBackend>) `polarity<-`(<MsBackend>) precScanNum(<MsBackend>) precursorCharge(<MsBackend>) precursorIntensity(<MsBackend>) precursorMz(<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>) longForm(<MsBackend>) MsBackendDataFrame() backendInitialize(<MsBackendDataFrame>) MsBackendHdf5Peaks() MsBackendMemory() backendInitialize(<MsBackendMemory>) MsBackendMzR()

Mass spectrometry data backends

MsBackendCached() backendInitialize(<MsBackendCached>) dataStorage(<MsBackendCached>) extractByIndex(<MsBackendCached>,<ANY>) 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>) precScanNum(<MsBackendCached>) precursorCharge(<MsBackendCached>) precursorIntensity(<MsBackendCached>) precursorMz(<MsBackendCached>) rtime(<MsBackendCached>) `rtime<-`(<MsBackendCached>) scanIndex(<MsBackendCached>) smoothed(<MsBackendCached>) `smoothed<-`(<MsBackendCached>)

Base MsBackend class providing data caching mechanism

Spectra(<missing>) Spectra(<MsBackend>) Spectra(<character>) Spectra(<ANY>) setBackend(<Spectra>,<MsBackend>) export(<Spectra>) dataStorageBasePath(<Spectra>) `dataStorageBasePath<-`(<Spectra>)

The Spectra class to manage and access MS data

processingLog() scalePeaks() addProcessing(<Spectra>) applyProcessing(<Spectra>) bin(<Spectra>) containsMz(<Spectra>) containsNeutralLoss(<Spectra>) entropy(<Spectra>) entropy(<ANY>) pickPeaks(<Spectra>) replaceIntensitiesBelow(<Spectra>) reset(<Spectra>) smooth(<Spectra>) spectrapply(<Spectra>)

Data manipulation and analysis methods

chunkapply()

Apply a function stepwise to chunks of data

combinePeaks(<Spectra>)

Aggregating and combining mass peaks data

combinePeaksData()

Combine peaks with similar m/z across spectra

concatenateSpectra() combineSpectra() joinSpectraData() c(<Spectra>) cbind2(<Spectra>,<dataframeOrDataFrameOrmatrix>) split(<Spectra>,<ANY>)

Merging, aggregating and splitting Spectra

compareSpectra(<Spectra>,<Spectra>) compareSpectra(<Spectra>,<missing>)

Spectra similarity calculations

countIdentifications()

Count the number of identifications per scan

estimatePrecursorIntensity(<Spectra>)

Estimate Precursor Intensities

estimatePrecursorMz()

Estimating precursor m/z valus for DDA data

fillCoreSpectraVariables()

Fill spectra data with columns for missing core variables

filterFourierTransformArtefacts fft_spectrum

Fast fourier transform artefact filter

deisotopeSpectra() reduceSpectra() filterPrecursorMaxIntensity() filterPrecursorIsotopes() filterPrecursorPeaks() dropNaSpectraVariables(<Spectra>) selectSpectraVariables(<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>) filterRanges(<Spectra>) filterValues(<Spectra>)

Filter and subset Spectra objects

filterPeaksRanges()

Filter peaks based on spectra and peaks variable ranges

fragmentGroupIndex()

Mass fragmentation collections of each full scan

joinPeaks() joinPeaksGnps() joinPeaksNone()

Join (map) peaks of two spectra

PrecursorMzParam() neutralLoss(<Spectra>,<PrecursorMzParam>)

Calculate Neutral Loss Spectra

computeMzDeltas() plotMzDelta()

MZ delta Quality Control

precursorPurity()

Calculating Precursor Purity for MS2 spectra

processingChunkSize(<Spectra>) `processingChunkSize<-`(<Spectra>) processingChunkFactor(<Spectra>) backendBpparam(<Spectra>)

Parallel and chunk-wise processing of Spectra

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

Plotting Spectra

asDataFrame() acquisitionNum(<Spectra>) centroided(<Spectra>) `centroided<-`(<Spectra>) collisionEnergy(<Spectra>) `collisionEnergy<-`(<Spectra>) coreSpectraVariables() dataOrigin(<Spectra>) `dataOrigin<-`(<Spectra>) dataStorage(<Spectra>) intensity(<Spectra>) ionCount(<Spectra>) isCentroided(<Spectra>) isEmpty(<Spectra>) isolationWindowLowerMz(<Spectra>) `isolationWindowLowerMz<-`(<Spectra>) isolationWindowTargetMz(<Spectra>) `isolationWindowTargetMz<-`(<Spectra>) isolationWindowUpperMz(<Spectra>) `isolationWindowUpperMz<-`(<Spectra>) length(<Spectra>) lengths(<Spectra>) longForm(<Spectra>) msLevel(<Spectra>) mz(<Spectra>) peaksData(<Spectra>) peaksVariables(<Spectra>) polarity(<Spectra>) `polarity<-`(<Spectra>) precScanNum(<Spectra>) precursorCharge(<Spectra>) precursorIntensity(<Spectra>) precursorMz(<Spectra>) `precursorMz<-`(<Spectra>) rtime(<Spectra>) `rtime<-`(<Spectra>) scanIndex(<Spectra>) smoothed(<Spectra>) `smoothed<-`(<Spectra>) spectraData(<Spectra>) `spectraData<-`(<Spectra>) spectraNames(<Spectra>) `spectraNames<-`(<Spectra>) spectraVariables(<Spectra>) tic(<Spectra>) uniqueMsLevels(<Spectra>) `$`(<Spectra>) `$<-`(<Spectra>) `[[`(<Spectra>) `[[<-`(<Spectra>)

Accessing mass spectrometry data

spectraVariableMapping() `spectraVariableMapping<-`()

Mapping between spectra variables and data file fields