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rformassspectrometry / MsIO

Serializing/importing mass spectrometry data objects eventually using language-agnostic formats.
https://rformassspectrometry.github.io/MsIO
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alabaster-based file formats #12

Closed jorainer closed 2 months ago

jorainer commented 3 months ago

This issue refers to issue #9

alabaster defines a framework to save and load R objects to standard file formats (JSON and HDF5). While I'm not particularly happy with the HDF5 export, because external software might actually have issues using that, it would be good to support (also) these formats. Especially, because we can re-use a lot of the already existing export/import functions for standard data types.

jorainer commented 3 months ago

Development of this is ongoing in the alabaster branch. So far, as a proof of principle, I've implemented methods for MsBackendMzR and Spectra. Next will be MsExperiment and XcmsExperiment. A key to these will be to ensure, especially for on-disk MS backends, that we can restore the objects also when the original data files or the storage of the object itself was moved to another computer or file system.

jorainer commented 2 months ago

Done.