This package is considered a duplicate. The official version of this package is found at:https://bioc.r-universe.dev/ProtGenerics

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]>

ProtGenerics_1.39.2.tar.gz
ProtGenerics_1.39.2.zip(r-4.7)ProtGenerics_1.39.2.zip(r-4.6)ProtGenerics_1.39.2.zip(r-4.5)
ProtGenerics_1.39.2.tgz(r-4.6-any)ProtGenerics_1.39.2.tgz(r-4.5-any)
ProtGenerics_1.39.2.tar.gz(r-4.7-any)ProtGenerics_1.39.2.tar.gz(r-4.6-any)
ProtGenerics_1.39.2.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
ProtGenerics/json (API)

# Install 'ProtGenerics' in R:

install.packages('ProtGenerics', repos = c('https://rformassspectrometry.r-universe.dev', 'https://cloud.r-project.org'))

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

On BioConductor:ProtGenerics-1.45.0(bioc 3.24)ProtGenerics-1.44.0(bioc 3.23)

infrastructure proteomics massspectrometry bioconductor mass-spectrometry metabolomics

7.47 score 8 stars 208 packages 13 scripts 137 exports 0 dependencies

Last updated from:0103c319a1. Checks:9 OK. Indexed: no.

Target	Result	Time
linux-devel-x86_64	OK	108
source / vignettes	OK	186
linux-release-x86_64	OK	92
macos-release-arm64	OK	74
macos-oldrel-arm64	OK	75
windows-devel	OK	69
windows-release	OK	66
windows-oldrel	OK	68
wasm-release	OK	88

Exports:accessions acquisitionNum addProcessing adjacencyMatrix aggregateFeatures alignRt analyser analyserDetails analyzer analyzerDetails applyProcessing as.list backendBpparam backendInitialize backendMerge backendParallelFactor bin calculateFragments centroided centroided<-chromatogram chromatograms collisionEnergy collisionEnergy<-combineFeatures compareChromatograms compareSpectra compounds database dataOrigin dataOrigin<-dataStorage dataStorage<-detectorType estimatePrecursorIntensity executeProcessingStep expemail exptitle extractByIndex filterAcquisitionNum filterDataOrigin filterDataStorage filterEmptySpectra filterFeatures filterIntensity filterIsolationWindow filterMsLevel filterMz filterMzRange filterMzValues filterNA filterPolarity filterPrecursorCharge filterPrecursorMz filterPrecursorMzRange filterPrecursorMzValues filterPrecursorScan filterProductMz filterProductMzRange filterProductMzValues filterRanges filterRt filterSpectra filterValues impute instrumentCustomisations instrumentManufacturer instrumentModel intensity intensity<-ionCount ions ionSource ionSourceDetails isCentroided isolationWindowLowerMz isolationWindowLowerMz<-isolationWindowTargetMz isolationWindowTargetMz<-isolationWindowUpperMz isolationWindowUpperMz<-isReadOnly mass modifications msInfo msLevel msLevel<-mz mz<-peaks peaks<-peaksData peaksData<-peaksVariables peptides polarity polarity<-precAcquisitionNum precScanNum precursorCharge precursorCharge<-precursorIntensity precursorIntensity<-precursorMz precursorMz<-processingChunkFactor processingChunkSize processingChunkSize<-processingData processingData<-ProcessingStep productMz productMz<-proteins psms quantify rtime rtime<-scanIndex scans setBackend smooth smoothed smoothed<-spectra spectra<-spectraData spectraData<-spectraNames spectraNames<-spectrapply spectraVariables supportsSetBackend tic tolerance uniqueMsLevels writeMSData

Dependencies:

Citation

Development and contributors

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