Allow more complex experimental designs

[sneumann]

Currently, the study_variable is a single list of levels:
https://hupo-psi.github.io/mzTab/2_0-metabolomics-release/mzTab_format_specification_2_0-M_release.html#study_variable1-n
any complex design with multiple experimental factors (e.g. Genotype x treatment x timepoint) can not be expressed.
Yours, Steffen

[nilshoffmann]

Current situation:

[nilshoffmann]

Suggested solution: adding -group as an additional attribute to study variable:

[nilshoffmann]

What we may not be fixing is the unorthodox naming of "study_variable" which should probably rather be named "study_variable_factor_level". Introducing "group" or "factor" would fix the primary issue, which is the lack of the top level grouping, but not the naming issue.

[sneumann]

Indeed, to maintain backwards-compatibility, we should fix the naming issue by good documentation and examples :-)

[philouail]

I know this is an old issue, but please go through the different steps of the template below, to make it easy for us to understand what to do next with this:

Is your feature request related to a problem? Please describe.
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Submitter Tasks

• Provide a pull request (Please add the link)
• Schema: Update mzTab_m_openapi.yml (View File)
• Specification: Update mzTab_format_specification_2_1-M.adoc with an example (View File)
• Example files: if possible, modify an existing or add a new example file (Existing example files)

Maintainer & WG Tasks

• Triage: Assign labels and Milestones to this issue.
• Discuss and review and approve PR.

Next Steps, once we reach an agreement on the changes above:

• Create a downstream issue in the jmzTab-m repo (https://github.com/lifs-tools/jmzTab-m/issues)
• Implement and test changes in jmzTab-M
• Implement changes in R & Python implementations

[philouail]

#77