Package: Chromatograms 0.2.0

Philippine Louail

Chromatograms: Infrastructure for Chromatographic Mass Spectrometry Data

The Chromatograms packages defines a 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:Laurent Gatto [aut], Johannes Rainer [aut], Philippine Louail [aut, cre]

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Chromatograms.pdf |Chromatograms.html✨
Chromatograms/json (API)

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

Peer review:

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

On CRAN:

infrastructureproteomicsmassspectrometrymetabolomics

3.60 score 1 stars 1 scripts 50 exports 10 dependencies

Last updated 13 days agofrom:38da022476. Checks:OK: 5 WARNING: 1 NOTE: 1. Indexed: yes.

TargetResultDate
Doc / VignettesOKNov 08 2024
R-4.5-winNOTENov 08 2024
R-4.5-linuxWARNINGNov 08 2024
R-4.4-winOKNov 08 2024
R-4.4-macOKNov 08 2024
R-4.3-winOKNov 08 2024
R-4.3-macOKNov 08 2024

Exports:backendInitializebackendMergebackendParallelFactorChromBackendMemorychromDatachromData<-chromIndexchromIndex<-chromVariablescollisionEnergycollisionEnergy<-coreChromVariablescorePeaksVariablesdataOrigindataOrigin<-dataStoragedataStorage<-fillCoreChromVariablesintensityintensity<-isEmptyisReadOnlymsLevelmsLevel<-mzmz<-mzMaxmzMax<-mzMinmzMin<-peaksDatapeaksData<-precursorMzprecursorMz<-precursorMzMaxprecursorMzMax<-precursorMzMinprecursorMzMin<-productMzproductMz<-productMzMaxproductMzMax<-productMzMinproductMzMin<-resetrtimertime<-splitvalidChromDatavalidPeaksData

Dependencies:BiocGenericsclueclustergenericsIRangesMASSMsCoreUtilsProtGenericsRcppS4Vectors

Creating new ChromBackend classes for Chromatograms

Rendered fromcreating-backend-classes.Rmdusingknitr::rmarkdownon Nov 08 2024.

Last update: 2024-11-07
Started: 2024-03-27

Readme and manuals

Help Manual

Help pageTopics
Improved in-memory Chromatographic data backendbackendInitialize,ChromBackendMemory-method ChromBackendMemory
Chromatographic MS Data Backends$,ChromBackend-method $<-,ChromBackend-method backendInitialize,ChromBackend-method backendMerge,ChromBackend-method backendMerge,list-method backendParallelFactor,ChromBackend-method ChromBackend ChromBackend-class ChromBackendMemory-class chromData chromData,ChromBackend-method chromData<- chromData<-,ChromBackend-method chromIndex chromIndex,ChromBackend-method chromIndex<- chromIndex<-,ChromBackend-method chromVariables chromVariables,ChromBackend-method collisionEnergy,ChromBackend-method collisionEnergy<-,ChromBackend-method coreChromVariables corePeaksVariables dataOrigin,ChromBackend-method dataOrigin<-,ChromBackend-method dataStorage,ChromBackend-method dataStorage<-,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 mzMax,ChromBackend-method mzMax<- mzMax<-,ChromBackend-method mzMin mzMin,ChromBackend-method mzMin<- mzMin<-,ChromBackend-method peaksData,ChromBackend-method peaksData<-,ChromBackend-method peaksVariables,ChromBackend-method precursorMz,ChromBackend-method precursorMz<-,ChromBackend-method precursorMzMax precursorMzMax,ChromBackend-method precursorMzMax<- precursorMzMax<-,ChromBackend-method precursorMzMin precursorMzMin,ChromBackend-method precursorMzMin<- precursorMzMin<-,ChromBackend-method productMz,ChromBackend-method productMz<-,ChromBackend-method productMzMax productMzMax,ChromBackend-method productMzMax<- productMzMax<-,ChromBackend-method productMzMin productMzMin,ChromBackend-method productMzMin<- productMzMin<-,ChromBackend-method reset reset,ChromBackend-method rtime,ChromBackend-method rtime<-,ChromBackend-method split,ChromBackend,ANY-method [,ChromBackend-method