Generic infrastructure for Bioconductor mass spectrometry packages

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Documentation for package ‘ProtGenerics’ version 1.40.0

• DESCRIPTION file.
• Package NEWS.

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