NAMESPACE

# Generated by roxygen2: do not edit by hand

export(MsBackendCached)
export(MsBackendDataFrame)
export(MsBackendHdf5Peaks)
export(MsBackendMemory)
export(MsBackendMzR)
export(PrecursorMzParam)
export(asDataFrame)
export(chunkapply)
export(combinePeaksData)
export(combineSpectra)
export(computeMzDeltas)
export(concatenateSpectra)
export(coreSpectraVariables)
export(countIdentifications)
export(deisotopeSpectra)
export(estimatePrecursorMz)
export(filterPeaksRanges)
export(filterPrecursorIsotopes)
export(filterPrecursorMaxIntensity)
export(filterPrecursorPeaks)
export(joinPeaks)
export(joinPeaksGnps)
export(joinPeaksNone)
export(joinSpectraData)
export(plotMzDelta)
export(plotSpectra)
export(plotSpectraOverlay)
export(ppm)
export(processingLog)
export(reduceSpectra)
export(scalePeaks)
export(spectraVariableMapping)
exportClasses(MsBackend)
exportClasses(MsBackendCached)
exportClasses(MsBackendDataFrame)
exportClasses(MsBackendMemory)
exportClasses(MsBackendMzR)
exportClasses(Spectra)
exportMethods("$")
exportMethods("$<-")
exportMethods("[")
exportMethods("[[")
exportMethods("[[<-")
exportMethods("centroided<-")
exportMethods("collisionEnergy<-")
exportMethods("dataOrigin<-")
exportMethods("dataStorage<-")
exportMethods("dataStorageBasePath<-")
exportMethods("intensity<-")
exportMethods("isolationWindowLowerMz<-")
exportMethods("isolationWindowTargetMz<-")
exportMethods("isolationWindowUpperMz<-")
exportMethods("msLevel<-")
exportMethods("mz<-")
exportMethods("peaksData<-")
exportMethods("polarity<-")
exportMethods("precursorMz<-")
exportMethods("processingChunkSize<-")
exportMethods("rtime<-")
exportMethods("smoothed<-")
exportMethods("spectraData<-")
exportMethods("spectraNames<-")
exportMethods(Spectra)
exportMethods(acquisitionNum)
exportMethods(addProcessing)
exportMethods(applyProcessing)
exportMethods(backendBpparam)
exportMethods(backendInitialize)
exportMethods(backendMerge)
exportMethods(backendParallelFactor)
exportMethods(backendRequiredSpectraVariables)
exportMethods(bin)
exportMethods(c)
exportMethods(cbind2)
exportMethods(centroided)
exportMethods(collisionEnergy)
exportMethods(combinePeaks)
exportMethods(compareSpectra)
exportMethods(containsMz)
exportMethods(containsNeutralLoss)
exportMethods(dataOrigin)
exportMethods(dataStorage)
exportMethods(dataStorageBasePath)
exportMethods(dropNaSpectraVariables)
exportMethods(entropy)
exportMethods(estimatePrecursorIntensity)
exportMethods(export)
exportMethods(extractByIndex)
exportMethods(filterAcquisitionNum)
exportMethods(filterDataOrigin)
exportMethods(filterDataStorage)
exportMethods(filterEmptySpectra)
exportMethods(filterFourierTransformArtefacts)
exportMethods(filterIntensity)
exportMethods(filterIsolationWindow)
exportMethods(filterMsLevel)
exportMethods(filterMzRange)
exportMethods(filterMzValues)
exportMethods(filterPolarity)
exportMethods(filterPrecursorCharge)
exportMethods(filterPrecursorMz)
exportMethods(filterPrecursorMzRange)
exportMethods(filterPrecursorMzValues)
exportMethods(filterPrecursorScan)
exportMethods(filterRanges)
exportMethods(filterRt)
exportMethods(filterValues)
exportMethods(intensity)
exportMethods(ionCount)
exportMethods(isCentroided)
exportMethods(isEmpty)
exportMethods(isReadOnly)
exportMethods(isolationWindowLowerMz)
exportMethods(isolationWindowTargetMz)
exportMethods(isolationWindowUpperMz)
exportMethods(length)
exportMethods(lengths)
exportMethods(msLevel)
exportMethods(mz)
exportMethods(neutralLoss)
exportMethods(peaksData)
exportMethods(peaksVariables)
exportMethods(pickPeaks)
exportMethods(plotSpectraMirror)
exportMethods(polarity)
exportMethods(precScanNum)
exportMethods(precursorCharge)
exportMethods(precursorIntensity)
exportMethods(precursorMz)
exportMethods(processingChunkFactor)
exportMethods(processingChunkSize)
exportMethods(replaceIntensitiesBelow)
exportMethods(reset)
exportMethods(rtime)
exportMethods(scanIndex)
exportMethods(selectSpectraVariables)
exportMethods(setBackend)
exportMethods(show)
exportMethods(smooth)
exportMethods(smoothed)
exportMethods(spectraData)
exportMethods(spectraNames)
exportMethods(spectraVariables)
exportMethods(spectrapply)
exportMethods(split)
exportMethods(supportsSetBackend)
exportMethods(tic)
exportMethods(uniqueMsLevels)
importClassesFrom(IRanges,IRanges)
importClassesFrom(IRanges,NumericList)
importClassesFrom(ProtGenerics,Param)
importClassesFrom(ProtGenerics,ProcessingStep)
importClassesFrom(S4Vectors,DataFrame)
importFrom(BiocGenerics,updateObject)
importFrom(BiocParallel,SerialParam)
importFrom(BiocParallel,bplapply)
importFrom(BiocParallel,bpparam)
importFrom(IRanges,NumericList)
importFrom(MetaboCoreUtils,isotopicSubstitutionMatrix)
importFrom(MetaboCoreUtils,isotopologues)
importFrom(MsCoreUtils,between)
importFrom(MsCoreUtils,closest)
importFrom(MsCoreUtils,coefMA)
importFrom(MsCoreUtils,coefSG)
importFrom(MsCoreUtils,coefWMA)
importFrom(MsCoreUtils,common)
importFrom(MsCoreUtils,common_path)
importFrom(MsCoreUtils,entropy)
importFrom(MsCoreUtils,group)
importFrom(MsCoreUtils,i2index)
importFrom(MsCoreUtils,join)
importFrom(MsCoreUtils,join_gnps)
importFrom(MsCoreUtils,localMaxima)
importFrom(MsCoreUtils,ndotproduct)
importFrom(MsCoreUtils,nentropy)
importFrom(MsCoreUtils,noise)
importFrom(MsCoreUtils,ppm)
importFrom(MsCoreUtils,rbindFill)
importFrom(MsCoreUtils,refineCentroids)
importFrom(MsCoreUtils,vapply1c)
importFrom(MsCoreUtils,vapply1d)
importFrom(MsCoreUtils,vapply1l)
importFrom(ProtGenerics,ProcessingStep)
importFrom(ProtGenerics,executeProcessingStep)
importFrom(ProtGenerics,smooth)
importFrom(S4Vectors,DataFrame)
importFrom(S4Vectors,SimpleList)
importFrom(S4Vectors,make_zero_col_DFrame)
importFrom(fs,path_sanitize)
importFrom(grDevices,dev.flush)
importFrom(grDevices,dev.hold)
importFrom(grDevices,n2mfrow)
importFrom(grDevices,xy.coords)
importFrom(graphics,abline)
importFrom(graphics,axis)
importFrom(graphics,box)
importFrom(graphics,hist)
importFrom(graphics,par)
importFrom(graphics,plot.new)
importFrom(graphics,plot.window)
importFrom(graphics,plot.xy)
importFrom(graphics,segments)
importFrom(graphics,strwidth)
importFrom(graphics,text)
importFrom(graphics,title)
importFrom(methods,"slot<-")
importFrom(methods,.hasSlot)
importFrom(methods,.valueClassTest)
importFrom(methods,as)
importFrom(methods,callNextMethod)
importFrom(methods,existsMethod)
importFrom(methods,is)
importFrom(methods,new)
importFrom(methods,setAs)
importFrom(methods,validObject)
importFrom(stats,approx)
importFrom(stats,cor)
importFrom(stats,quantile)
importFrom(stats,weighted.mean)
importFrom(tools,file_path_sans_ext)
importFrom(utils,capture.output)
importFrom(utils,combn)
importFrom(utils,packageVersion)
importMethodsFrom(BiocParallel,bplapply)
importMethodsFrom(BiocParallel,bpmapply)
importMethodsFrom(IRanges,extractList)
importMethodsFrom(IRanges,replaceROWS)
importMethodsFrom(ProtGenerics,"centroided<-")
importMethodsFrom(ProtGenerics,"collisionEnergy<-")
importMethodsFrom(ProtGenerics,"dataOrigin<-")
importMethodsFrom(ProtGenerics,"dataStorage<-")
importMethodsFrom(ProtGenerics,"intensity<-")
importMethodsFrom(ProtGenerics,"isolationWindowLowerMz<-")
importMethodsFrom(ProtGenerics,"isolationWindowTargetMz<-")
importMethodsFrom(ProtGenerics,"isolationWindowUpperMz<-")
importMethodsFrom(ProtGenerics,"msLevel<-")
importMethodsFrom(ProtGenerics,"mz<-")
importMethodsFrom(ProtGenerics,"peaksData<-")
importMethodsFrom(ProtGenerics,"polarity<-")
importMethodsFrom(ProtGenerics,"precursorMz<-")
importMethodsFrom(ProtGenerics,"processingChunkSize<-")
importMethodsFrom(ProtGenerics,"rtime<-")
importMethodsFrom(ProtGenerics,"smoothed<-")
importMethodsFrom(ProtGenerics,"spectraData<-")
importMethodsFrom(ProtGenerics,"spectraNames<-")
importMethodsFrom(ProtGenerics,acquisitionNum)
importMethodsFrom(ProtGenerics,addProcessing)
importMethodsFrom(ProtGenerics,applyProcessing)
importMethodsFrom(ProtGenerics,backendBpparam)
importMethodsFrom(ProtGenerics,backendInitialize)
importMethodsFrom(ProtGenerics,backendMerge)
importMethodsFrom(ProtGenerics,backendParallelFactor)
importMethodsFrom(ProtGenerics,bin)
importMethodsFrom(ProtGenerics,centroided)
importMethodsFrom(ProtGenerics,collisionEnergy)
importMethodsFrom(ProtGenerics,compareSpectra)
importMethodsFrom(ProtGenerics,dataOrigin)
importMethodsFrom(ProtGenerics,dataStorage)
importMethodsFrom(ProtGenerics,estimatePrecursorIntensity)
importMethodsFrom(ProtGenerics,extractByIndex)
importMethodsFrom(ProtGenerics,filterAcquisitionNum)
importMethodsFrom(ProtGenerics,filterDataOrigin)
importMethodsFrom(ProtGenerics,filterDataStorage)
importMethodsFrom(ProtGenerics,filterEmptySpectra)
importMethodsFrom(ProtGenerics,filterIntensity)
importMethodsFrom(ProtGenerics,filterIsolationWindow)
importMethodsFrom(ProtGenerics,filterMsLevel)
importMethodsFrom(ProtGenerics,filterMzRange)
importMethodsFrom(ProtGenerics,filterMzValues)
importMethodsFrom(ProtGenerics,filterPolarity)
importMethodsFrom(ProtGenerics,filterPrecursorCharge)
importMethodsFrom(ProtGenerics,filterPrecursorMz)
importMethodsFrom(ProtGenerics,filterPrecursorMzRange)
importMethodsFrom(ProtGenerics,filterPrecursorMzValues)
importMethodsFrom(ProtGenerics,filterPrecursorScan)
importMethodsFrom(ProtGenerics,filterRanges)
importMethodsFrom(ProtGenerics,filterRt)
importMethodsFrom(ProtGenerics,filterValues)
importMethodsFrom(ProtGenerics,intensity)
importMethodsFrom(ProtGenerics,ionCount)
importMethodsFrom(ProtGenerics,isCentroided)
importMethodsFrom(ProtGenerics,isReadOnly)
importMethodsFrom(ProtGenerics,isolationWindowLowerMz)
importMethodsFrom(ProtGenerics,isolationWindowTargetMz)
importMethodsFrom(ProtGenerics,isolationWindowUpperMz)
importMethodsFrom(ProtGenerics,msLevel)
importMethodsFrom(ProtGenerics,mz)
importMethodsFrom(ProtGenerics,peaksData)
importMethodsFrom(ProtGenerics,peaksVariables)
importMethodsFrom(ProtGenerics,polarity)
importMethodsFrom(ProtGenerics,precScanNum)
importMethodsFrom(ProtGenerics,precursorCharge)
importMethodsFrom(ProtGenerics,precursorIntensity)
importMethodsFrom(ProtGenerics,precursorMz)
importMethodsFrom(ProtGenerics,processingChunkFactor)
importMethodsFrom(ProtGenerics,processingChunkSize)
importMethodsFrom(ProtGenerics,rtime)
importMethodsFrom(ProtGenerics,scanIndex)
importMethodsFrom(ProtGenerics,setBackend)
importMethodsFrom(ProtGenerics,smoothed)
importMethodsFrom(ProtGenerics,spectraData)
importMethodsFrom(ProtGenerics,spectraNames)
importMethodsFrom(ProtGenerics,spectraVariables)
importMethodsFrom(ProtGenerics,spectrapply)
importMethodsFrom(ProtGenerics,supportsSetBackend)
importMethodsFrom(ProtGenerics,tic)
importMethodsFrom(ProtGenerics,uniqueMsLevels)
importMethodsFrom(S4Vectors,"$")
importMethodsFrom(S4Vectors,"$<-")
importMethodsFrom(S4Vectors,"[")
importMethodsFrom(S4Vectors,"[[")
importMethodsFrom(S4Vectors,extractROWS)
importMethodsFrom(S4Vectors,isEmpty)
importMethodsFrom(S4Vectors,lapply)
importMethodsFrom(S4Vectors,split)
importMethodsFrom(methods,cbind2)
importMethodsFrom(methods,show)