Package: ProtGenerics 1.39.2

Laurent Gatto

ProtGenerics: Generic infrastructure for Bioconductor mass spectrometry packages

S4 generic functions and classes needed by Bioconductor proteomics packages.

Authors:Laurent Gatto <[email protected]>, Johannes Rainer <[email protected]>

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ProtGenerics.pdf |ProtGenerics.html✨
ProtGenerics/json (API)
NEWS

# Install 'ProtGenerics' in R:
install.packages('ProtGenerics', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Bug tracker:https://github.com/rformassspectrometry/protgenerics/issues

On BioConductor:ProtGenerics-1.39.1(bioc 3.21)ProtGenerics-1.38.0(bioc 3.20)

infrastructureproteomicsmassspectrometrybioconductormass-spectrometrymetabolomics

9.54 score 8 stars 189 packages 4 scripts 19k downloads 137 exports 0 dependencies

Last updated 17 hours agofrom:0103c319a1. Checks:7 OK. Indexed: yes.

TargetResultLatest binary
Doc / VignettesOKJan 16 2025
R-4.5-winOKJan 16 2025
R-4.5-linuxOKJan 16 2025
R-4.4-winOKJan 16 2025
R-4.4-macOKJan 16 2025
R-4.3-winOKJan 16 2025
R-4.3-macOKJan 16 2025

Exports:accessionsacquisitionNumaddProcessingadjacencyMatrixaggregateFeaturesalignRtanalyseranalyserDetailsanalyzeranalyzerDetailsapplyProcessingas.listbackendBpparambackendInitializebackendMergebackendParallelFactorbincalculateFragmentscentroidedcentroided<-chromatogramchromatogramscollisionEnergycollisionEnergy<-combineFeaturescompareChromatogramscompareSpectracompoundsdatabasedataOrigindataOrigin<-dataStoragedataStorage<-detectorTypeestimatePrecursorIntensityexecuteProcessingStepexpemailexptitleextractByIndexfilterAcquisitionNumfilterDataOriginfilterDataStoragefilterEmptySpectrafilterFeaturesfilterIntensityfilterIsolationWindowfilterMsLevelfilterMzfilterMzRangefilterMzValuesfilterNAfilterPolarityfilterPrecursorChargefilterPrecursorMzfilterPrecursorMzRangefilterPrecursorMzValuesfilterPrecursorScanfilterProductMzfilterProductMzRangefilterProductMzValuesfilterRangesfilterRtfilterSpectrafilterValuesimputeinstrumentCustomisationsinstrumentManufacturerinstrumentModelintensityintensity<-ionCountionsionSourceionSourceDetailsisCentroidedisolationWindowLowerMzisolationWindowLowerMz<-isolationWindowTargetMzisolationWindowTargetMz<-isolationWindowUpperMzisolationWindowUpperMz<-isReadOnlymassmodificationsmsInfomsLevelmsLevel<-mzmz<-peakspeaks<-peaksDatapeaksData<-peaksVariablespeptidespolaritypolarity<-precAcquisitionNumprecScanNumprecursorChargeprecursorCharge<-precursorIntensityprecursorIntensity<-precursorMzprecursorMz<-processingChunkFactorprocessingChunkSizeprocessingChunkSize<-processingDataprocessingData<-ProcessingStepproductMzproductMz<-proteinspsmsquantifyrtimertime<-scanIndexscanssetBackendsmoothsmoothedsmoothed<-spectraspectra<-spectraDataspectraData<-spectraNamesspectraNames<-spectrapplyspectraVariablessupportsSetBackendtictoleranceuniqueMsLevelswriteMSData

Dependencies:

Readme and manuals

Help Manual

Help pageTopics
General backend methodsbackendBpparam backendInitialize backendMerge backendParallelFactor isReadOnly setBackend supportsSetBackend
Extracting elements by indexextractByIndex
Filter featuresfilterFeatures
Filter SpectrafilterSpectra
Generic parameter classas.list,Param-method Param Param-class show,Param-method
Get or set MS peak datapeaksData peaksData<- peaksVariables
Processing QueueaddProcessing applyProcessing processingChunkFactor processingChunkSize processingChunkSize<- processingQueue
Processing stepcharacterOrFunction-class executeProcessingStep ProcessingStep ProcessingStep-class show,ProcessingStep-method
S4 generic functions for Bioconductor proteomics infrastructureProtGenerics-package accessions acquisitionNum adjacencyMatrix aggregateFeatures alignRt analyser analyserDetails analyzer analyzerDetails bin calculateFragments centroided centroided<- chromatogram chromatograms collisionEnergy collisionEnergy<- combineFeatures compareChromatograms compareSpectra compounds database dataOrigin dataOrigin<- dataStorage dataStorage<- detectorType estimatePrecursorIntensity expemail exptitle filterAcquisitionNum filterDataOrigin filterDataStorage filterEmptySpectra filterIntensity filterIsolationWindow filterMsLevel filterMz filterMzRange filterMzValues filterNA filterPolarity filterPrecursorCharge filterPrecursorMz filterPrecursorMzRange filterPrecursorMzValues filterPrecursorScan filterProductMz filterProductMzRange filterProductMzValues filterRanges filterRt filterValues impute instrumentCustomisations instrumentManufacturer instrumentModel intensity intensity<- ionCount ions ionSource ionSourceDetails isCentroided isolationWindowLowerMz isolationWindowLowerMz<- isolationWindowTargetMz isolationWindowTargetMz<- isolationWindowUpperMz isolationWindowUpperMz<- mass modifications msInfo msLevel msLevel<- mz mz<- peaks peaks<- peptides polarity polarity<- precAcquisitionNum precScanNum precursorCharge precursorCharge<- precursorIntensity precursorIntensity<- precursorMz precursorMz<- processingData processingData<- productMz productMz<- proteins ProtGenerics psms quantify rtime rtime<- scanIndex scans smooth smoothed smoothed<- spectra spectra<- spectraData spectraData<- spectraNames spectraNames<- spectrapply spectraVariables tic tolerance uniqueMsLevels writeMSData