chore(tmt): Adjust TMT documentation

[tonywu1999]

Motivation and context

TMT documentation examples used data from the MSstatsTMT package. The examples now use CSV files bundled with MSstatsConvert, which matches the current data source.

Changes

• Updated tmt_summarization_loop examples.
• Updated tmt_model examples.
• Replaced data() calls with data.table::fread().
• Kept the example workflows unchanged.
• Made no functional code changes.

Tests

• No unit tests were added or modified.
• Changes are limited to documentation examples.

Coding guideline violations

• 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: 014aeeb8-b774-4c81-929c-5df8fb0b9a0e

📥 Commits

Reviewing files that changed from the base of the PR and between 5cc87ea and 3c94647.

📒 Files selected for processing (3)

• R/main_calculations.R
• man/tmt_model.Rd
• man/tmt_summarization_loop.Rd

Included review availability: Your plan provides up to 1 included review per hour; 0 remain after this review.

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📝 Walkthrough

Walkthrough

The PDTMT examples now load raw and annotation CSV files from MSstatsConvert with data.table::fread(). The processing examples remain unchanged.

Changes

PDTMT Documentation Examples

Layer / File(s)	Summary
Documentation example input loading R/main_calculations.R, man/tmt_model.Rd, man/tmt_summarization_loop.Rd	The examples replace MSstatsTMT dataset loading with data.table::fread() calls for CSV files in MSstatsConvert.

Priority: ⬇️ Low

Estimated code review effort: 1 (Trivial) | ~2 minutes

Merge Risk: ⚪ Minimal · up to 3c946

PDTMT examples now load CSV inputs from MSstatsConvert rather than MSstatsTMT datasets. The documentation updates are consistent across source and generated manual pages, with no remaining merge-readiness risk identified.

🚥 Pre-merge checks | ✅ 5

✅ Passed checks (5 passed)

Check name	Status	Explanation
Description Check	✅ Passed	Check skipped - CodeRabbit’s high-level summary is enabled.
Title check	✅ Passed	The title clearly and concisely describes the documentation changes for TMT examples.
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.

✨ Finishing Touches

🧪 Generate unit tests (beta)

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

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