docs(fragpipe): Update vignettes and documentation for Fragpipe converter

Vitek-Lab / MSstatsPTM

Post Translational Modification (PTM) Significance Analysis in shotgun mass spectrometry-based proteomic experiments

https://vitek-lab.github.io/MSstatsPTM/

Artistic License 2.0

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Closed tonywu1999 closed 3 months ago

tonywu1999 commented 4 months ago

In this issue, it was unclear if the Fragpipe converter supported label free.

We also saw the purity parameter in Fragpipe and nobody on the dev team had any idea what that meant.

Add vignettes for label free for the Fragpipe converter. The user gave us some sample data which I added to the MSstatsPTM package (however, the user didn't have global profiling data since it didn't matter to them).
Update documentation on the purity parameter.

tonywu1999 commented 3 months ago

Devon is chill with this