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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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addition of MetaboLightsParam #17

Closed philouail closed 2 months ago

philouail commented 2 months ago

Here is the code in order to get a full MsExperiment object with spectra and sample data from the database.

I changed from merged() to cbind(), it is more stable i found and does not show warnings because of duplicated columns.

Tell me what you think about the extra parameters I implemented in order to simplify the sampleData !

Also see my note in the code (in the helper function description) about the duplicated ontology column automatic numbering so we can discuss it.

Lastly, unfortunately the GHA beaks because of MsBackendMetaboLights, is there a workaround ? For me the unit tests work locally.

Any other things I'm missing also ? Should there be an offline parameter similar to MsBackendMetaboLights ?

philouail commented 2 months ago

@jorainer the tests pass, but not for linux aha, do you know what is happening ?