# Generic infrastructure for Bioconductor mass spectrometry packages

## Documentation for package ‘ProtGenerics’ version 1.44.0

- DESCRIPTION file
- Package NEWS
- Package README

## Help Pages

A B C D E F I M P Q R S T U W

ProtGenerics-package | S4 generic functions for Bioconductor proteomics infrastructure

## -- A --

accessions | S4 generic functions for Bioconductor proteomics infrastructure
acquisitionNum | S4 generic functions for Bioconductor proteomics infrastructure
addProcessing | Processing Queue
adjacencyMatrix | S4 generic functions for Bioconductor proteomics infrastructure
aggregateFeatures | S4 generic functions for Bioconductor proteomics infrastructure
alignRt | S4 generic functions for Bioconductor proteomics infrastructure
analyser | S4 generic functions for Bioconductor proteomics infrastructure
analyserDetails | S4 generic functions for Bioconductor proteomics infrastructure
analyzer | S4 generic functions for Bioconductor proteomics infrastructure
analyzerDetails | S4 generic functions for Bioconductor proteomics infrastructure
applyProcessing | Processing Queue
as.list-method | Generic parameter class

## -- B --

backendBpparam | General backend methods
backendInitialize | General backend methods
backendMerge | General backend methods
backendParallelFactor | General backend methods
bin | S4 generic functions for Bioconductor proteomics infrastructure

## -- C --

calculateFragments | S4 generic functions for Bioconductor proteomics infrastructure
centroided | S4 generic functions for Bioconductor proteomics infrastructure
centroided<- | S4 generic functions for Bioconductor proteomics infrastructure
characterOrFunction-class | Processing step
chromatogram | S4 generic functions for Bioconductor proteomics infrastructure
chromatograms | S4 generic functions for Bioconductor proteomics infrastructure
collisionEnergy | S4 generic functions for Bioconductor proteomics infrastructure
collisionEnergy<- | S4 generic functions for Bioconductor proteomics infrastructure
combineFeatures | S4 generic functions for Bioconductor proteomics infrastructure
compareChromatograms | S4 generic functions for Bioconductor proteomics infrastructure
compareSpectra | S4 generic functions for Bioconductor proteomics infrastructure
compounds | S4 generic functions for Bioconductor proteomics infrastructure

## -- D --

database | S4 generic functions for Bioconductor proteomics infrastructure
dataOrigin | S4 generic functions for Bioconductor proteomics infrastructure
dataOrigin<- | S4 generic functions for Bioconductor proteomics infrastructure
dataStorage | S4 generic functions for Bioconductor proteomics infrastructure
dataStorage<- | S4 generic functions for Bioconductor proteomics infrastructure
detectorType | S4 generic functions for Bioconductor proteomics infrastructure

## -- E --

estimatePrecursorIntensity | S4 generic functions for Bioconductor proteomics infrastructure
executeProcessingStep | Processing step
expemail | S4 generic functions for Bioconductor proteomics infrastructure
exptitle | S4 generic functions for Bioconductor proteomics infrastructure
extractByIndex | Extracting elements by index

## -- F --

filterAcquisitionNum | S4 generic functions for Bioconductor proteomics infrastructure
filterDataOrigin | S4 generic functions for Bioconductor proteomics infrastructure
filterDataStorage | S4 generic functions for Bioconductor proteomics infrastructure
filterEmptySpectra | S4 generic functions for Bioconductor proteomics infrastructure
filterFeatures | Filter features
filterIntensity | S4 generic functions for Bioconductor proteomics infrastructure
filterIsolationWindow | S4 generic functions for Bioconductor proteomics infrastructure
filterMsLevel | S4 generic functions for Bioconductor proteomics infrastructure
filterMz | S4 generic functions for Bioconductor proteomics infrastructure
filterMzRange | S4 generic functions for Bioconductor proteomics infrastructure
filterMzValues | S4 generic functions for Bioconductor proteomics infrastructure
filterNA | S4 generic functions for Bioconductor proteomics infrastructure
filterPolarity | S4 generic functions for Bioconductor proteomics infrastructure
filterPrecursorCharge | S4 generic functions for Bioconductor proteomics infrastructure
filterPrecursorMz | S4 generic functions for Bioconductor proteomics infrastructure
filterPrecursorMzRange | S4 generic functions for Bioconductor proteomics infrastructure
filterPrecursorMzValues | S4 generic functions for Bioconductor proteomics infrastructure
filterPrecursorScan | S4 generic functions for Bioconductor proteomics infrastructure
filterProductMz | S4 generic functions for Bioconductor proteomics infrastructure
filterProductMzRange | S4 generic functions for Bioconductor proteomics infrastructure
filterProductMzValues | S4 generic functions for Bioconductor proteomics infrastructure
filterRanges | S4 generic functions for Bioconductor proteomics infrastructure
filterRt | S4 generic functions for Bioconductor proteomics infrastructure
filterSpectra | Filter Spectra
filterValues | S4 generic functions for Bioconductor proteomics infrastructure

## -- I --

impute | S4 generic functions for Bioconductor proteomics infrastructure
instrumentCustomisations | S4 generic functions for Bioconductor proteomics infrastructure
instrumentManufacturer | S4 generic functions for Bioconductor proteomics infrastructure
instrumentModel | S4 generic functions for Bioconductor proteomics infrastructure
intensity | S4 generic functions for Bioconductor proteomics infrastructure
intensity<- | S4 generic functions for Bioconductor proteomics infrastructure
ionCount | S4 generic functions for Bioconductor proteomics infrastructure
ions | S4 generic functions for Bioconductor proteomics infrastructure
ionSource | S4 generic functions for Bioconductor proteomics infrastructure
ionSourceDetails | S4 generic functions for Bioconductor proteomics infrastructure
isCentroided | S4 generic functions for Bioconductor proteomics infrastructure
isolationWindowLowerMz | S4 generic functions for Bioconductor proteomics infrastructure
isolationWindowLowerMz<- | S4 generic functions for Bioconductor proteomics infrastructure
isolationWindowTargetMz | S4 generic functions for Bioconductor proteomics infrastructure
isolationWindowTargetMz<- | S4 generic functions for Bioconductor proteomics infrastructure
isolationWindowUpperMz | S4 generic functions for Bioconductor proteomics infrastructure
isolationWindowUpperMz<- | S4 generic functions for Bioconductor proteomics infrastructure
isReadOnly | General backend methods

## -- M --

mass | S4 generic functions for Bioconductor proteomics infrastructure
modifications | S4 generic functions for Bioconductor proteomics infrastructure
msInfo | S4 generic functions for Bioconductor proteomics infrastructure
msLevel | S4 generic functions for Bioconductor proteomics infrastructure
msLevel<- | S4 generic functions for Bioconductor proteomics infrastructure
mz | S4 generic functions for Bioconductor proteomics infrastructure
mz<- | S4 generic functions for Bioconductor proteomics infrastructure

## -- P --

Param | Generic parameter class
Param-class | Generic parameter class
peaks | S4 generic functions for Bioconductor proteomics infrastructure
peaks<- | S4 generic functions for Bioconductor proteomics infrastructure
peaksData | Get or set MS peak data
peaksData<- | Get or set MS peak data
peaksVariables | Get or set MS peak data
peptides | S4 generic functions for Bioconductor proteomics infrastructure
polarity | S4 generic functions for Bioconductor proteomics infrastructure
polarity<- | S4 generic functions for Bioconductor proteomics infrastructure
precAcquisitionNum | S4 generic functions for Bioconductor proteomics infrastructure
precScanNum | S4 generic functions for Bioconductor proteomics infrastructure
precursorCharge | S4 generic functions for Bioconductor proteomics infrastructure
precursorCharge<- | S4 generic functions for Bioconductor proteomics infrastructure
precursorIntensity | S4 generic functions for Bioconductor proteomics infrastructure
precursorIntensity<- | S4 generic functions for Bioconductor proteomics infrastructure
precursorMz | S4 generic functions for Bioconductor proteomics infrastructure
precursorMz<- | S4 generic functions for Bioconductor proteomics infrastructure
processingChunkFactor | Processing Queue
processingChunkSize | Processing Queue
processingChunkSize<- | Processing Queue
processingData | S4 generic functions for Bioconductor proteomics infrastructure
processingData<- | S4 generic functions for Bioconductor proteomics infrastructure
processingQueue | Processing Queue
ProcessingStep | Processing step
ProcessingStep-class | Processing step
productMz | S4 generic functions for Bioconductor proteomics infrastructure
productMz<- | S4 generic functions for Bioconductor proteomics infrastructure
proteins | S4 generic functions for Bioconductor proteomics infrastructure
ProtGenerics | S4 generic functions for Bioconductor proteomics infrastructure
psms | S4 generic functions for Bioconductor proteomics infrastructure

## -- Q --

quantify | S4 generic functions for Bioconductor proteomics infrastructure

## -- R --

rtime | S4 generic functions for Bioconductor proteomics infrastructure
rtime<- | S4 generic functions for Bioconductor proteomics infrastructure

## -- S --

scanIndex | S4 generic functions for Bioconductor proteomics infrastructure
scans | S4 generic functions for Bioconductor proteomics infrastructure
setBackend | General backend methods
show-method | Generic parameter class
show-method | Processing step
smooth | S4 generic functions for Bioconductor proteomics infrastructure
smoothed | S4 generic functions for Bioconductor proteomics infrastructure
smoothed<- | S4 generic functions for Bioconductor proteomics infrastructure
spectra | S4 generic functions for Bioconductor proteomics infrastructure
spectra<- | S4 generic functions for Bioconductor proteomics infrastructure
spectraData | S4 generic functions for Bioconductor proteomics infrastructure
spectraData<- | S4 generic functions for Bioconductor proteomics infrastructure
spectraNames | S4 generic functions for Bioconductor proteomics infrastructure
spectraNames<- | S4 generic functions for Bioconductor proteomics infrastructure
spectrapply | S4 generic functions for Bioconductor proteomics infrastructure
spectraVariables | S4 generic functions for Bioconductor proteomics infrastructure
supportsSetBackend | General backend methods

## -- T --

tic | S4 generic functions for Bioconductor proteomics infrastructure
tolerance | S4 generic functions for Bioconductor proteomics infrastructure

## -- U --

uniqueMsLevels | S4 generic functions for Bioconductor proteomics infrastructure

## -- W --

writeMSData | S4 generic functions for Bioconductor proteomics infrastructure