Generic infrastructure for Bioconductor mass spectrometry packages


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Documentation for package ‘ProtGenerics’ version 1.30.0

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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 S4 generic functions for Bioconductor proteomics infrastructure
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
as.list-method Generic parameter class

-- B --

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 --

executeProcessingStep Processing step
expemail S4 generic functions for Bioconductor proteomics infrastructure
exptitle S4 generic functions for Bioconductor proteomics infrastructure

-- 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
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
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
filterPrecursorScan S4 generic functions for Bioconductor proteomics infrastructure
filterProductMz S4 generic functions for Bioconductor proteomics infrastructure
filterRt 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

-- 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
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
processingData S4 generic functions for Bioconductor proteomics infrastructure
processingData<- S4 generic functions for Bioconductor proteomics infrastructure
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
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

-- T --

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

-- U --

uniqueMsLevel S4 generic functions for Bioconductor proteomics infrastructure

-- W --

writeMSData S4 generic functions for Bioconductor proteomics infrastructure