docs(ptm): Fix documentation regarding MSstatsPTM groupComparisonPTM

[tonywu1999]

Motivation and Context

The MSstatsPTM package's groupComparisonPTM function API changed and no longer accepts the data.type = "LabelFree" argument. MSstatsShiny documentation examples referenced the deprecated argument, producing incorrect examples. This PR updates examples to reflect the current MSstatsPTM API so documentation is accurate and runnable.

Solution Summary

• Remove the deprecated data.type = "LabelFree" argument from examples calling MSstatsPTM::groupComparisonPTM, leaving only the required summary data argument.
• Regenerate the corresponding Rd documentation to match the updated example.
• Remove a repository GitHub Actions workflow (.github/workflows/codium-pr-agent.yml).

Detailed Changes

• R/main_calculations.R

  • Updated example in the apply_adj-related documentation to:
    model = MSstatsPTM::groupComparisonPTM(MSstatsPTM::summary.data)
    (removed data.type = "LabelFree" from the example).
  • No functional code changes; only the @examples text was modified.
  • File present and verified.

• man/apply_adj.Rd

  • Regenerated Rd file now showing the updated example that omits data.type = "LabelFree":
    model = MSstatsPTM::groupComparisonPTM(MSstatsPTM::summary.data)
    apply_adj(model$PTM.Model, model$PROTEIN.Model)
  • Reflects the roxygen2-generated documentation from R/main_calculations.R.

• .github/workflows/codium-pr-agent.yml

  • Workflow file removed from the repository (Codium AI PR agent workflow).

Tests

• No unit tests were added or modified. This change is documentation-only (examples and Rd) plus removal of a CI workflow; package behavior and logic are unchanged.

Coding Guidelines / Violations

• No coding guideline violations introduced by this PR.
• Documentation updated using roxygen2/Rd conventions.
• Note: Removing the CI workflow is a repository maintenance decision — verify maintainers intend to remove that automation before merging.

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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: 082d7b6b-6b22-4e0f-90ae-2ba7fc1d182a

📥 Commits

Reviewing files that changed from the base of the PR and between 8aa53db and 9685dd7.

📒 Files selected for processing (1)

• .github/workflows/codium-pr-agent.yml

💤 Files with no reviewable changes (1)

• .github/workflows/codium-pr-agent.yml

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📝 Walkthrough

Walkthrough

Removed a redundant data.type = "LabelFree" argument from groupComparisonPTM examples in two documentation files and deleted the .github/workflows/codium-pr-agent.yml GitHub Actions workflow. No functional code changes.

Changes

Cohort / File(s)	Summary
Documentation Example Updates R/main_calculations.R, man/apply_adj.Rd	Removed the data.type = "LabelFree" argument from groupComparisonPTM example calls.
CI Workflow Removal .github/workflows/codium-pr-agent.yml	Deleted a PR-triggered GitHub Actions workflow file (Codium AI PR agent).

Estimated code review effort

🎯 2 (Simple) | ⏱️ ~10 minutes

Poem

🐇 I nudged an arg away, neat and light,
Examples now hop with clearer sight,
A workflow waved goodbye, a soft thump—
Fewer lines, a cleaner jump! 🥕✨

🚥 Pre-merge checks | ✅ 3

✅ Passed checks (3 passed)

Check name	Status	Explanation
Description Check	✅ Passed	Check skipped - CodeRabbit’s high-level summary is enabled.
Title check	✅ Passed	The title accurately describes the main changes: documentation fixes in PTM-related files regarding the groupComparisonPTM function call (removing the data.type argument).
Docstring Coverage	✅ Passed	No functions found in the changed files to evaluate docstring coverage. Skipping docstring coverage check.

_{✏️ Tip: You can configure your own custom pre-merge checks in the settings.}

✨ Finishing Touches

🧪 Generate unit tests (beta)

• Create PR with unit tests
• Post copyable unit tests in a comment
• Commit unit tests in branch fix-ptm

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[github-actions]

PR Reviewer Guide 🔍

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⏱️ Estimated effort to review: 1 🔵⚪⚪⚪⚪

🧪 No relevant tests

🔒 No security concerns identified

⚡ Recommended focus areas for review Example Robustness The updated example calls MSstatsPTM::groupComparisonPTM(MSstatsPTM::summary.data) without specifying data.type. Please double-check that the default data.type is stable across supported MSstatsPTM versions and that this example reliably runs during documentation checks. #' model = MSstatsPTM::groupComparisonPTM(MSstatsPTM::summary.data) #' apply_adj(model$PTM.Model, model$PROTEIN.Model) R CMD Check Ensure the example is appropriate for automated execution (e.g., it is fast, deterministic, and does not require external resources). If groupComparisonPTM is computationally heavy, consider guarding it with \dontrun{} or \donttest{} as appropriate to avoid CRAN/R CMD check timeouts. model = MSstatsPTM::groupComparisonPTM(MSstatsPTM::summary.data) apply_adj(model$PTM.Model, model$PROTEIN.Model)

[github-actions]

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