fix documentation for dataProcess and groupComparison

[ShonenAsh]

Motivation and Context

Fixed parts of dataProcess() and groupComparison() documentation to match the utils_output.R.

The @return blocks of the above functions return different/more objects (verified against live output on DDARawData) that weren't documented.

Changes

• Renamed NumMeasuredFeatures to NumMeasuredFeature in both @return blocks.
  • I can also change the output column in utils_output.R instead but I chose to do it here to avoid breaking any downstream code.
• Documented previously missing pieces: the SummaryMethod element of dataProcess()'s return value, the LABEL column in ProteinLevelData and ModelQC, the remove column in FeatureLevelData, and the columns that appear only for featureSubset = "highQuality" or label-based data.
• Clarified that MissingPercentage and ImputationPercentage are proportions between 0 and 1.
• @param raw now states it takes a data.frame, not the name of a data set.

Testing

No changes required here. I ran devtools::document()

Checklist Before Requesting a Review

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

Motivation and context

The documentation for dataProcess() and groupComparison() did not match the current output fields. This update aligns the source documentation and generated .Rd files with the implemented outputs.

Changes

• Updated dataProcess() documentation.
• Specified that raw accepts an MSstats long-format data frame.
• Renamed NumMeasuredFeatures to NumMeasuredFeature.
• Documented SummaryMethod, LABEL, remove, and conditional feature fields.
• Clarified missingness and imputation values as proportions from 0 to 1.
• Updated groupComparison() documentation with matching field names and label information.
• Regenerated the affected .Rd files.

Tests

• No unit tests were added or modified.
• Existing tests cover dataProcess() and groupComparison().
• devtools::document() completed without new warnings.

Coding guidelines

• No coding guideline violations were identified.

[coderabbitai]

No actionable comments were generated in the recent review. 🎉

ℹ️ Recent review info

⚙️ Run configuration

Configuration used: Organization UI

Review profile: CHILL

Plan: Advanced

Run ID: edd87d70-ee01-4c50-af4e-cc7bea9e3270

📥 Commits

Reviewing files that changed from the base of the PR and between 21fee47 and 936fcc4.

📒 Files selected for processing (4)

• R/dataProcess.R
• R/groupComparison.R
• man/dataProcess.Rd
• man/groupComparison.Rd

Included review availability: Your plan provides up to 2 included reviews per hour; 1 remains after this review.

---

📝 Walkthrough

Walkthrough

The changes update dataProcess and groupComparison documentation. They describe current input formats, return elements, conditional columns, labeling fields, measured-feature names, and missingness proportions.

Changes

Documentation alignment

Layer / File(s)	Summary
dataProcess input and output schema R/dataProcess.R, man/dataProcess.Rd	Documents MSstats long-format input, three return elements, conditional feature columns, protein-level fields, and SummaryMethod.
groupComparison result schema R/groupComparison.R, man/groupComparison.Rd	Documents percentage ranges, isotopic labeling, the NumMeasuredFeature name, and missingness fields in ComparisonResult and ModelQC.

Priority: ⬇️ Low

Estimated code review effort: 1 (Trivial) | ~3 minutes

Merge Risk: ⚪ Minimal · up to 936fc

This updates dataProcess and groupComparison documentation to accurately describe current inputs, outputs, field names, labels, and missingness proportions. No current merge-blocking risk remains.

Suggested reviewers: tonywu1999

🚥 Pre-merge checks | ✅ 5

✅ Passed checks (5 passed)

Check name	Status	Explanation
Docstring Coverage	✅ Passed	No functions found in the changed files to evaluate docstring coverage. Skipping docstring coverage check. Docstring coverage is scoped to functions touched by this diff. Analyzed 0 functions across 0…
Linked Issues check	✅ Passed	Check skipped because no linked issues were found for this pull request.
Out of Scope Changes check	✅ Passed	Check skipped because no linked issues were found for this pull request.
Title check	✅ Passed	The title clearly and concisely identifies the documentation updates for dataProcess and groupComparison.
Description check	✅ Passed	The description includes motivation, detailed changes, testing information, and a completed checklist. It matches the documented scope of the pull request.

✨ Finishing Touches

🧪 Generate unit tests (beta)

• Create PR with unit tests

---

Thanks for using CodeRabbit! It's free for OSS, and your support helps us grow. If you like it, consider giving us a shout-out.

❤️ Share

• X
• Mastodon
• Reddit
• LinkedIn

_{A rabbit updates each careful line
Fields and labels now align
Three returns hop into view
Missingness measures follow too
The docs are tidy, clear, and bright}

_{Comment @coderabbitai help to get the list of available commands.}