[Pruthvi] Update Vignette & Documentation for MSstatsBioNet

[tonywu1999]

Context

MSstatsBioNet needs better vignettes that show users how to use MSstatsBioNet via various use cases. One package that notably has really good vignettes is MSstatsPTM. We can refer to Biostrings when creating our vignettes.

Subtasks

• Identify datasets that would be suitable for a vignette, e.g. Talus dataset for perturbations, CCRCC dataset for discovery.
• Add an introduction on the purpose of perturbation and discovery experiments, outlining what successful interpretation looks like for each experiment type.
• Write a full workflow demonstration of MSstats followed by MSstatsBioNet for a perturbation experiment and discovery experiment.
  • Using MSstats, ensure abundances are normalized when processing data in vignette.
• Document existing issues, e.g. getSubnetworkFromIndra not working in MSstatsShiny
• PR & Merge

Acceptance Criteria

Vignette has been updated and merged.