Package: Chromatograms 0.5.0

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'))

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

On CRAN:

infrastructure proteomics massspectrometry metabolomics

4.15 score 1 stars 3 scripts 60 exports 19 dependencies

Last updated 21 days agofrom:4fef76ff29. Checks:1 OK, 1 NOTE, 6 ERROR. Indexed: yes.

Target	Result	Latest binary
Doc / Vignettes	OK	Feb 18 2025
R-4.5-win	ERROR	Feb 18 2025
R-4.5-mac	ERROR	Feb 18 2025
R-4.5-linux	NOTE	Feb 18 2025
R-4.4-win	ERROR	Feb 18 2025
R-4.4-mac	ERROR	Feb 18 2025
R-4.3-win	ERROR	Feb 18 2025
R-4.3-mac	ERROR	Feb 18 2025

Exports:applyProcessing backendBpparam backendInitialize backendMerge backendParallelFactor Chromatograms ChromBackendMemory ChromBackendMzR chromData chromData<-chromIndex chromIndex<-chromVariables collisionEnergy collisionEnergy<-coreChromVariables corePeaksVariables dataOrigin dataOrigin<-fillCoreChromVariables filterChromData filterPeaksData intensity intensity<-isEmpty isReadOnly msLevel msLevel<-mz mz<-mzMax mzMax<-mzMin mzMin<-peaksData peaksData<-precursorMz precursorMz<-precursorMzMax precursorMzMax<-precursorMzMin precursorMzMin<-processingChunkFactor processingChunkSize processingChunkSize<-productMz productMz<-productMzMax productMzMax<-productMzMin productMzMin<-reset rtime rtime<-setBackend show split supportsSetBackend validChromData validPeaksData

Dependencies:BH BiocGenerics BiocParallel clue cluster codetools cpp11 formatR futile.logger futile.options generics IRanges lambda.r MASS MsCoreUtils ProtGenerics Rcpp S4Vectors snow

Creating new ChromBackend classes for Chromatograms

Rendered fromcreating-backend-classes.Rmdusingknitr::rmarkdownon Feb 18 2025.

Last update: 2025-02-18
Started: 2024-03-27

Using and understanding a Chromatograms object

Rendered fromusing-a-chromatograms-object.Rmdusingknitr::rmarkdownon Feb 18 2025.

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

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
The Chromatograms class to manage and access chromatographic data	$,Chromatograms-method $<-,Chromatograms-method Chromatograms Chromatograms-class setBackend,Chromatograms,ChromBackend-method
Improved in-memory Chromatographic data backend	backendInitialize,ChromBackendMemory-method ChromBackendMemory
Chromatographic Data Backend for Reading mzML Files	backendInitialize,ChromBackendMzR-method ChromBackendMzR
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
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 chromData,ChromBackend-method chromData<-,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 filterChromData,ChromBackend-method filterPeaksData,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 data	filterPeaksData filterPeaksData,Chromatograms-method intensity,Chromatograms-method intensity<-,Chromatograms-method peaksData peaksData,Chromatograms-method peaksData<-,Chromatograms-method peaksVariables peaksVariables,Chromatograms-method rtime,Chromatograms-method rtime<-,Chromatograms-method
Efficiently processing 'Chromatograms' objects.	addProcessing,Chromatograms-method applyProcessing,Chromatograms-method processingChunkFactor,Chromatograms-method processingChunkSize,Chromatograms-method processingChunkSize<-,Chromatograms-method processingQueue