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:
ProtGenerics_1.39.2.tar.gz
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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')) |
Bug tracker:https://github.com/rformassspectrometry/protgenerics/issues
On BioConductor:ProtGenerics-1.39.2(bioc 3.21)ProtGenerics-1.38.0(bioc 3.20)
infrastructureproteomicsmassspectrometrybioconductormass-spectrometrymetabolomics
Last updated 1 months agofrom:0103c319a1. Checks:8 OK. Indexed: yes.
| Target | Result | Latest binary |
|---|---|---|
| Doc / Vignettes | OK | Feb 15 2025 |
| R-4.5-win | OK | Feb 15 2025 |
| R-4.5-mac | OK | Feb 15 2025 |
| R-4.5-linux | OK | Feb 15 2025 |
| R-4.4-win | OK | Feb 15 2025 |
| R-4.4-mac | OK | Feb 15 2025 |
| R-4.3-win | OK | Feb 15 2025 |
| R-4.3-mac | OK | Feb 15 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 page | Topics |
|---|---|
| General backend methods | backendBpparam backendInitialize backendMerge backendParallelFactor isReadOnly setBackend supportsSetBackend |
| Extracting elements by index | extractByIndex |
| Filter features | filterFeatures |
| Filter Spectra | filterSpectra |
| Generic parameter class | as.list,Param-method Param Param-class show,Param-method |
| Get or set MS peak data | peaksData peaksData<- peaksVariables |
| Processing Queue | addProcessing applyProcessing processingChunkFactor processingChunkSize processingChunkSize<- processingQueue |
| Processing step | characterOrFunction-class executeProcessingStep ProcessingStep ProcessingStep-class show,ProcessingStep-method |
| S4 generic functions for Bioconductor proteomics infrastructure | ProtGenerics-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 |
