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alabaster-based file formats #12

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jorainer opened this issue Aug 2, 2024 · 2 comments
Closed

alabaster-based file formats #12

jorainer opened this issue Aug 2, 2024 · 2 comments
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jorainer commented Aug 2, 2024

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 jorainer self-assigned this Aug 2, 2024
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jorainer commented Aug 2, 2024

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 jorainer added the enhancement New feature or request label Aug 2, 2024
jorainer added a commit that referenced this issue Aug 8, 2024
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feat: add saveMsObject, readMsObject for MsExperiment and alabaster
05dfdfe 
- Add `saveMsObject()` and `readMsObject()` methods for `MsExperiment` objects
  and `AlabasterParam` (issue #12).
jorainer added a commit that referenced this issue Aug 9, 2024
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feat: add alabaster-based export/import for XcmsExperiment
2b0e9b1 
- Add `saveObject()`, `readObject()` methods as well as `saveMsObject()`,
  `readMsObject()` with `AlabasterParam` for *xcms* result object
  `XcmsExperiment` (issue #12).
jorainer added a commit that referenced this issue Aug 22, 2024
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Merge pull request #13 from rformassspectrometry/alabaster
385f74c 
Add alabaster support to MsIO (issue #12)
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Done.

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