Fix turnover

[tonywu1999]

Motivation and context

The turnover analysis workflow needed more robust peptide weighting and a documented, exported API for confidence and protein classification. The changes improve sparse-data handling and expose the supporting quality-control and classification functions.

Changes

• Added calculateConfidence, calculateQCScore, and classifyTurnoverProteins to the public API with documentation.
• Added documentation for kendall_monotonicity.
• Added a robust Kendall monotonicity helper that returns zero for sparse, missing, invalid, or zero-variance data.
• Updated peptide weighting to use the new monotonicity helper.
• Updated dplyr, stats, and ggplot2 imports.
• Refreshed roxygen2 configuration metadata.
• Updated dataset usage documentation.
• Expanded calculatePeptideWeights documentation with coverage diagnostics and scoring details.

Unit tests

No test additions or modifications are identified in the provided changes.

Coding guidelines

No coding-guideline violations are identified in the provided changes.

[coderabbitai]

No actionable comments were generated in the recent review. 🎉

ℹ️ Recent review info

⚙️ Run configuration

Configuration used: Organization UI

Review profile: CHILL

Plan: Pro

Run ID: 2eddd66b-e580-40a7-98bb-b807ea5a0569

📥 Commits

Reviewing files that changed from the base of the PR and between 08261c0 and bd83ab3.

📒 Files selected for processing (11)

• DESCRIPTION
• NAMESPACE
• R/ExperimentalDesignSimulation.R
• R/TPR_Power_Curve.R
• R/protein_turnover_ratio_helper.R
• man/DIA_MSstats_Normalized.Rd
• man/calculateConfidence.Rd
• man/calculatePeptideWeights.Rd
• man/calculateQCScore.Rd
• man/classifyTurnoverProteins.Rd
• man/kendall_monotonicity.Rd

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📝 Walkthrough

Walkthrough

The package now declares roxygen2 8.0.0 metadata, exports three additional functions, updates imports and documentation, and uses a sparse-data-safe Kendall monotonicity helper in peptide weighting.

Changes

Package API and scoring

Layer / File(s)	Summary
API metadata and documentation DESCRIPTION, NAMESPACE, R/ExperimentalDesignSimulation.R, R/TPR_Power_Curve.R, man/...	Roxygen metadata, exports, imports, plotting annotations, dataset usage, and documentation for confidence, QC scoring, and protein classification were updated.
Robust peptide monotonicity scoring R/protein_turnover_ratio_helper.R, man/calculatePeptideWeights.Rd, man/kendall_monotonicity.Rd	A Kendall monotonicity helper now returns zero for sparse, missing, or undefined inputs, and calculatePeptideWeights() uses it with expanded diagnostic documentation.

Estimated code review effort: 2 (Simple) | ~10 minutes

Possibly related PRs

• Vitek-Lab/MSstatsResponse#6: Updates overlapping ggplot2 roxygen imports in the TPR power-curve module.

Suggested labels: enhancement

Suggested reviewers: sarahszvetecz

Poem

I’m a bunny with a tidy new score,
Counting sparse points as zeros once more.
Roxygen blooms, exports take flight,
Kendall hops through missing data right.
Nibble, test, and ship tonight!

🚥 Pre-merge checks | ✅ 4 | ❌ 1

❌ Failed checks (1 inconclusive)

Check name	Status	Explanation	Resolution
Title check	❓ Inconclusive	The title is related to the turnover-related changes, but it is too vague to convey the main update.	Use a more specific title, such as adding the new turnover confidence/QC/classification work or the updated peptide weighting behavior.

✅ Passed checks (4 passed)

Check name	Status	Explanation
Description Check	✅ Passed	Check skipped - CodeRabbit’s high-level summary is enabled.
Docstring Coverage	✅ Passed	No functions found in the changed files to evaluate docstring coverage. Skipping docstring coverage check.
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.

✨ Finishing Touches

🧪 Generate unit tests (beta)

• Create PR with unit tests
• Commit unit tests in branch fix-turnover

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