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MsIO

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

The MsIO package supports serializing and restoring/importing mass spectrometry (MS) data objects to and from language agnostic file formats. Ultimately, this package aims at enabling an easier exchange of data and results between different software tools and programming languages.

R provides with the save() and load() functions a possibility to serialize (and later import) variables and objects to disk, but the data is stored in a R-specific binary format which is not easily readable by other programming languages or software tools. Exchange of data and results between programming languages and tools is however important to avoid the need to re-implement methodology and algorithms and make the most of existing software to create powerful analysis workflow.

The MsIO package defines generic export/import methods along with parameter objects that allow to select and configure the file format(s). Where possible, it is integrated with other approaches in Bioconductor such as the alabaster.base package. In particular MsIO will integrate with alabaster.base providing saveObject() methods for exporting/importing MS specific data objects to JSON file formats, but, on top of that, supporting serializing MS data objects in additional different formats and thus supporting specific file formats defined by other software.

Currently supported and implemented storage representations

The currently available export/data storage formats along with the respective parameter object to configure the export/import are listed below:

  • PlainTextParam: Export to or import from plain text files. For most objects the data is stored in simple tabulator delimited text files. Export/import can be configured with the PlainTextParam parameter class and is supported at present for MsBackendMzR and Spectra objects from the Spectra package, MsExperiment objects from the MsExperiment package and XcmsExperiment objects from the xcms package.

  • AlabasterParam: Export or import based on alabaster. The alabaster format stores the data in a structured way using standard file formats including HDF5 and JSON ensuring thus across programming language compatibility.

  • mzTabParam: xcms preprocessing results (i.e., from XcmsExperiment objects) can be exported in mzTab-M format.

  • MetaboLightsParam: Import MS data experiments (including MS data files) from the public MetaboLights repository.

Contributions

Contributions are highly welcome and should follow the contribution guidelines. Also, please check the coding style guidelines in the RforMassSpectrometry vignette.

License

The MsIO code is provided under a permissive Artistic 2.0 license. The documentation, including the manual pages and the vignettes, are distributed under a CC BY-SA license.