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Low level infrastructure to handle chromatographic data

Project Status: Active – The project has reached a stable, usable state and is being actively developed. years in bioc R-CMD-check-bioc codecov license

This package, part of the R for Mass Spectrometry initiative, provides a powerful and expandable infrastructure for handling and analysing chromatographic mass spectrometry (MS) data.

It will replace the legacy classes to handle chromatographic data in R provided by the MSnbase package.

This package is part of Bioconductor: https://bioconductor.org/packages/Chromatograms.

⚙️ General concept

A Chromatograms object is designed to contain multiple chromatographic data (i.e. chromatogram entities). The data will be stored linearly, i.e. as a long list of chromatograms. The Chromatograms object will be the main object for the end user, providing functionality to access, filter or process chromatographic data, with the actual chromatographic MS data being stored within backend classes. Different implementations of backend classes can be designed for high performance or low memory footprint.

The existing backend classes are:

  • ChromBackendMemory: a memory-based backend, storing the data in memory. This is the default backend and is used for testing purposes.

  • The ChromBackendMzR inherits all slots and methods from the base ChromBackendMemory backend, providing additional functionality for reading chromatographic data from mzML files.

  • ChromBackendSpectra: The ChromBackendSpectra inherits all slots and methods from the base ChromBackendMemory backend, providing additional functionality for reading chromatographic data from Spectra objects.

These backend are then handled on a user level by the Chromatograms class, which provides a unified interface to access and manipulate the chromatographic data.

⤵️ Installation 

install.packages("BiocManager")
BiocManager::install("Chromatograms")

🤝 Contribution

Please help us improving and completing the package! Any type of contribution welcome 👐 - including discussions, suggestions or actual code. Don’t be afraid - we’re friendly ☺️! 👉 get involved by opening an issue.

Please also check out the RforMassSpectrometry Contributions Guide.

📜 Code of Conduct

We follow the RforMassSpectrometry Code of Conduct to maintain an inclusive and respectful community.

License

This package is licensed under the Artistic 2.0 license: 📄 https://opensource.org/license/Artistic-2.0

Documentation (manuals, vignettes) is licensed under CC BY-NC-SA 4.0: 📄 https://creativecommons.org/licenses/by-nc-sa/4.0/

Funding information

Part of this work was funded by the European Union under the HORIZON-MSCA-2021 project 101073062: HUMAN – Harmonising and Unifying Blood Metabolic Analysis Networks.

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