docs(dataProcess+groupComparison): Add documentation on output tables of dataProcess and groupComparison

[tonywu1999]

User description

Motivation and Context

We've been getting a good amount of questions on the MSstats google groups on what certain columns mean in the output of dataProcess and groupComparison. We should add documentation.

Checklist Before Requesting a Review

• [x] I have read the MSstats contributing guidelines
• [x] My changes generate no new warnings
• [x] Any dependent changes have been merged and published in downstream modules
• [x] I have run the devtools::document() command after my changes and committed the added files

---

PR Type

Documentation

---

Description

• Added comprehensive documentation for the dataProcess function, detailing the structure and columns of the FeatureLevelData and ProteinLevelData return values.
• Enhanced the groupComparison function documentation by describing the components of the return value, including ComparisonResult, ModelQC, and FittedModel.
• Updated the corresponding Rd files to reflect these documentation improvements.

---

Changes walkthrough 📝

Relevant files

Documentation

dataProcess.R Add detailed return value documentation for `dataProcess` function R/dataProcess.R Added detailed documentation for the return value of the dataProcess function. Described the structure and columns of FeatureLevelData and ProteinLevelData. +39/-1    groupComparison.R Add detailed return value documentation for groupComparison function R/groupComparison.R Added detailed documentation for the return value of the groupComparison function. Described the structure and columns of ComparisonResult, ModelQC, and FittedModel. +36/-2    dataProcess.Rd Update documentation for `dataProcess` function return value man/dataProcess.Rd Updated documentation to include detailed description of the return value. Described the structure and columns of FeatureLevelData and ProteinLevelData. +39/-0    groupComparison.Rd Update documentation for `groupComparison` function return value man/groupComparison.Rd Updated documentation to include detailed description of the return value. Described the structure and columns of ComparisonResult, ModelQC, and FittedModel. +36/-2

---

💡 PR-Agent usage: Comment /help "your question" on any pull request to receive relevant information

[github-actions[bot]]

PR Reviewer Guide 🔍

Here are some key observations to aid the review process:

⏱️ Estimated effort to review: 2 🔵🔵⚪⚪⚪

🧪 No relevant tests

🔒 No security concerns identified

⚡ No major issues detected

[github-actions[bot]]

PR Code Suggestions ✨

No code suggestions found for the PR.