Package: Chromatograms 1.3.0

Philippine Louail

Chromatograms: Infrastructure for Chromatographic Mass Spectrometry Data

The Chromatograms packages defines an efficient infrastructure for storing and handling of chromatographic mass spectrometry data. It provides different implementations of *backends* to store and represent the data. Such backends can be optimized for small memory footprint or fast data access/processing. A lazy evaluation queue and chunk-wise processing capabilities ensure efficient analysis of also very large data sets.

Authors:Johannes Rainer [aut], Laurent Gatto [aut], Philippine Louail [aut, cre]

Chromatograms_1.3.0.tar.gz
Chromatograms_1.3.0.zip(r-4.7)Chromatograms_1.3.0.zip(r-4.6)Chromatograms_1.3.0.zip(r-4.5)
Chromatograms_1.3.0.tgz(r-4.6-any)Chromatograms_1.3.0.tgz(r-4.5-any)
Chromatograms_1.3.0.tar.gz(r-4.7-any)Chromatograms_1.3.0.tar.gz(r-4.6-any)
Chromatograms_1.3.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
Chromatograms/json (API)

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

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

On BioConductor:Chromatograms-1.3.0(bioc 3.24)Chromatograms-1.2.0(bioc 3.23)

infrastructuremetabolomicsmassspectrometryproteomics

7.04 score 3 stars 1 packages 27 scripts 73 exports 23 dependencies

Last updated from:811bdb411a. Checks:9 OK. Indexed: no.

TargetResultTimeFilesSyslog
linux-devel-x86_64OK290
source / vignettesOK261
linux-release-x86_64OK267
macos-release-arm64OK197
macos-oldrel-arm64OK202
windows-develOK330
windows-releaseOK319
windows-oldrelOK299
wasm-releaseOK163

Exports:applyProcessingbackendBpparambackendInitializebackendMergebackendParallelFactorChromatogramsChromBackendMemoryChromBackendMzRChromBackendSpectrachromDatachromData<-chromExtractchromIndexchromIndex<-chromSpectraIndexchromVariablescollisionEnergycollisionEnergy<-compareChromatogramsconcatenateChromatogramscoreChromVariablescorePeaksVariablesdataOrigindataOrigin<-extractByIndexfactorizefillCoreChromVariablesfilterChromDatafilterEmptyChromatogramsfilterPeaksDataimputePeaksDataintensityintensity<-isEmptyisReadOnlymatchRtimemsLevelmsLevel<-mzmz<-mzMaxmzMax<-mzMinmzMin<-peakBoundarypeaksDatapeaksData<-plotChromatogramsplotChromatogramsOverlayprecursorMzprecursorMz<-precursorMzMaxprecursorMzMax<-precursorMzMinprecursorMzMin<-processingChunkFactorprocessingChunkSizeprocessingChunkSize<-productMzproductMz<-productMzMaxproductMzMax<-productMzMinproductMzMin<-resetrtimertime<-setBackendshowsplitsupportsSetBackendvalidChromDatavalidPeaksData

Dependencies:BHBiocGenericsBiocParallelclueclustercodetoolscpp11data.tableformatRfsfutile.loggerfutile.optionsgenericsIRangeslambda.rMASSMetaboCoreUtilsMsCoreUtilsProtGenericsRcppS4VectorssnowSpectra

Creating new ChromBackend classes for Chromatograms

Rendered fromcreating-backend-classes.Rmdusingknitr::rmarkdownon Jun 03 2026.

Last update: 2025-07-14
Started: 2024-03-27

Using and understanding a Chromatograms object

Rendered fromusing-a-chromatograms-object.Rmdusingknitr::rmarkdownon Jun 03 2026.

Last update: 2026-04-02
Started: 2025-02-18

Readme and manuals

Help Manual

Help pageTopics
The Chromatograms class to manage and access chromatographic data$,Chromatograms-method $<-,Chromatograms-method Chromatograms Chromatograms,ChromBackendOrMissing-method Chromatograms,Spectra-method Chromatograms-class chromExtract chromExtract,Chromatograms-method factorize,Chromatograms-method filterEmptyChromatograms filterEmptyChromatograms,Chromatograms-method setBackend,Chromatograms,ChromBackend-method [,Chromatograms-method [<-,Chromatograms-method [[,Chromatograms-method [[<-,Chromatograms-method
Improved in-memory Chromatographic data backendbackendInitialize,ChromBackendMemory-method ChromBackendMemory
Chromatographic Data Backend for Reading mzML FilesbackendInitialize,ChromBackendMzR-method ChromBackendMzR
Chromatographic Data Backend for Spectra ObjectsbackendInitialize,ChromBackendSpectra-method ChromBackendSpectra chromSpectraIndex
Chromatographic Peaks Metadata.chromData chromData,Chromatograms-method chromData<- chromData<-,Chromatograms-method chromIndex chromIndex,Chromatograms-method chromIndex<- chromIndex<-,Chromatograms-method chromVariables chromVariables,Chromatograms-method chromVariables<- collisionEnergy collisionEnergy,Chromatograms-method collisionEnergy<- collisionEnergy<-,Chromatograms-method dataOrigin dataOrigin,Chromatograms-method dataOrigin<- dataOrigin<-,Chromatograms-method filterChromData filterChromData,Chromatograms-method length,Chromatograms-method msLevel msLevel,Chromatograms-method msLevel<- msLevel<-,Chromatograms-method mz mz,Chromatograms-method mz<- mz<-,Chromatograms-method mzMax mzMax,Chromatograms-method mzMax<- mzMax<-,Chromatograms-method mzMin mzMin,Chromatograms-method mzMin<- mzMin<-,Chromatograms-method precursorMz precursorMz,Chromatograms-method precursorMz<- precursorMz<-,Chromatograms-method precursorMzMax precursorMzMax,Chromatograms-method precursorMzMax<- precursorMzMax<-,Chromatograms-method precursorMzMin precursorMzMin,Chromatograms-method precursorMzMin<- precursorMzMin<-,Chromatograms-method productMz productMz,Chromatograms-method productMz<- productMz<-,Chromatograms-method productMzMax productMzMax,Chromatograms-method productMzMax<- productMzMax<-,Chromatograms-method productMzMin productMzMin,Chromatograms-method productMzMin<- productMzMin<-,Chromatograms-method
Merging, combining and splitting Chromatogramsc,Chromatograms-method concatenateChromatograms split,Chromatograms,ANY-method
Chromatographic MS Data Backends$,ChromBackend-method $<-,ChromBackend-method backendBpparam,ChromBackend-method backendInitialize,ChromBackend-method backendMerge,ChromBackend-method backendMerge,list-method backendParallelFactor,ChromBackend-method ChromBackend ChromBackend-class ChromBackendMemory-class ChromBackendMzR-class ChromBackendSpectra-class chromData,ChromBackend-method chromData<-,ChromBackend-method chromExtract,ChromBackend-method chromIndex,ChromBackend-method chromIndex<-,ChromBackend-method chromVariables,ChromBackend-method collisionEnergy,ChromBackend-method collisionEnergy<-,ChromBackend-method coreChromVariables corePeaksVariables dataOrigin,ChromBackend-method dataOrigin<-,ChromBackend-method extractByIndex extractByIndex,ChromBackend,ANY-method extractByIndex,ChromBackend,missing-method factorize factorize,ChromBackend-method filterChromData,ChromBackend-method filterEmptyChromatograms,ChromBackend-method filterPeaksData,ChromBackend-method imputePeaksData,ChromBackend-method intensity,ChromBackend-method intensity<-,ChromBackend-method isEmpty,ChromBackend-method isReadOnly,ChromBackend-method length,ChromBackend-method lengths,ChromBackend-method msLevel,ChromBackend-method msLevel<-,ChromBackend-method mz,ChromBackend-method mz<-,ChromBackend-method mzMax,ChromBackend-method mzMax<-,ChromBackend-method mzMin,ChromBackend-method mzMin<-,ChromBackend-method peaksData,ChromBackend-method peaksData<-,ChromBackend-method peaksVariables,ChromBackend-method precursorMz,ChromBackend-method precursorMz<-,ChromBackend-method precursorMzMax,ChromBackend-method precursorMzMax<-,ChromBackend-method precursorMzMin,ChromBackend-method precursorMzMin<-,ChromBackend-method productMz,ChromBackend-method productMz<-,ChromBackend-method productMzMax,ChromBackend-method productMzMax<-,ChromBackend-method productMzMin,ChromBackend-method productMzMin<-,ChromBackend-method reset,ChromBackend-method rtime,ChromBackend-method rtime<-,ChromBackend-method split,ChromBackend,ANY-method supportsSetBackend,ChromBackend-method [,ChromBackend-method [[,ChromBackend-method [[<-,ChromBackend-method
Chromatographic peaks datacompareChromatograms compareChromatograms,Chromatograms,Chromatograms-method compareChromatograms,Chromatograms,missing-method filterPeaksData filterPeaksData,Chromatograms-method imputePeaksData imputePeaksData,Chromatograms-method intensity,Chromatograms-method intensity<-,Chromatograms-method lengths,Chromatograms-method matchRtime peakBoundary peakBoundary,Chromatograms-method peaksData peaksData,Chromatograms-method peaksData<-,Chromatograms-method peaksVariables peaksVariables,Chromatograms-method rtime,Chromatograms-method rtime<-,Chromatograms-method
Plot chromatogramsplotChromatograms plotChromatogramsOverlay
Efficiently processing 'Chromatograms' objects.addProcessing,Chromatograms-method applyProcessing,Chromatograms-method processingChunkFactor,Chromatograms-method processingChunkSize,Chromatograms-method processingChunkSize<-,Chromatograms-method processingQueue