Addition of MzTabParam for export in .mztab format

sneumann / xcms

This is the git repository matching the Bioconductor package xcms: LC/MS and GC/MS Data Analysis

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Addition of MzTabParam for export in .mztab format #718

Open philouail opened 5 months ago

philouail commented 5 months ago

Here is the PR for the implementation of mztab-m export using the storeResults generic function combined with a param object of class MzTabParam .

For now, the export format only has the mandatory field available (as well as possibility to add opt_ columns for the SMF table. In the future more metadata rows could be implemented if it makes sense from the format of XcmsExperiment object.

Any feedback and correction is welcomed.

sneumann commented 5 months ago

Hi, thanks for that PR!

[ ] Can you confirm the generated mzTab-M validates with https://apps.lifs-tools.org/mztabvalidator/ ?
[x] Can you also confirm import works with mztab <- MSnbase::MzTab(data_file) ?
[x] Can you check that MetaboAnalyst is happy: https://www.metaboanalyst.ca/MetaboAnalyst/upload/StatUploadView.xhtml
[ ] Can you check that GNPS is happy: https://ccms-ucsd.github.io/GNPSDocumentation/featurebasedmolecularnetworking-with-mztab-m/

Yours, Steffen