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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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(Proper) support for mzTab-M #357

Open sneumann opened 5 years ago

sneumann commented 5 years ago

Hi, the 6.4. Small Molecule Feature (SMF) Section (https://hupo-psi.github.io/mzTab/2_0-metabolomics-draft/mzTab_format_specification_2_0-M_draft.html#small-molecule-feature-smf-section) of the mzTab-M format can be used to encode information on the features. We already have a prototype xcmsSet mzTab-export in https://github.com/sneumann/xcms/blob/master/R/writemztab.R. It would be great to have "proper" support for writing (and reading !) mzTab-M also for the XCMS3 / MSnBase / CAMERA export. For the latter, we need sneumann/CAMERA/issues/35, and eventually this could integrate output from MetFrag(R), see ipb-halle/MetFragR/issues/23 Yours, Steffen

jorainer commented 5 years ago

Sounds great! I'll have a look at mzTab export/import. Most likely that has to go into xcms, not MSnbase.

jorainer commented 5 years ago

To keep this issue up-to-date: after metaRbolomics we (@nilshoffmann) agreed that it might be best to import mzTabR (or whatever the name will be) in xcms, have the functionality there to create a MzTabObject from an XCMSnExp object and use the mzTabR functionality to serialize the MzTabObject to mzTab-m.

nilshoffmann commented 5 years ago

The package now lives at lifs-tools/rmztab-m