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sneumann / xcms

This is the git repository matching the Bioconductor package xcms: LC/MS and GC/MS Data Analysis
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feat: creation of new generic function so save XcmsExperiment object #698

Closed philouail closed 7 months ago

philouail commented 8 months ago

Hi so this is just a draft, but I thought it might be easier to discuss here. I might need a bit of back and forth as it's the first time I do that :) Hope it's fine for you to do it like that. I'll also leave it as draft to avoid confusion.

See my comments for the parts that I'm confused about !

philouail commented 8 months ago

Oh and also I tried to do the necessary changes in description and NEWS files, but can you check if it looks OK ? Maybe there's different rules for XCMS compared to the other packages I contributed. And I have to look into this NAMESPACE thing, to see how to do it manually tomorrow.

jorainer commented 8 months ago

For the NAMESPACE, just add 

export RDataParam
exportMethods storeResults

that should be enough. Description and NEWS are OK - yes, there is a different format here, but what you added is fine.

philouail commented 8 months ago

Hi @sneumann so this PR is related to #693, it establish a new generics function storeResults that will allow to save xcms results objects into different format. This PR also implement the first format which is .RData with the RDataParam. I will then look into the Plain text file format and lastly MzTab-m they will each have they own param class and specific method.

Tell me if there is anything unclear or I need to change something.

sneumann commented 7 months ago

Cool, so ready to merge from my side.