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>) 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

joinPeaks() joinPeaksGnps() joinPeaksNone()

Join (map) peaks of two spectra

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

Calculate Neutral Loss Spectra

computeMzDeltas() plotMzDelta()

MZ delta Quality Control

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>) 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