Fix #185: thread censoredInt correctly and remove spurious unique() in exported script

[swaraj-neu]

Motivation and Context

Issue #185 identified two problems in the MSstatsShiny codebase:

1. The censoredInt parameter was not being properly threaded through the MSstatsHandleMissing function call in lf_summarization_loop, which was instead relying on a hardcoded missing value symbol
2. The exported script code generated by getDataCode() contained an unnecessary unique() deduplication step that was producing spurious behavior for non-PTM inputs

This PR fixes both issues by ensuring the censored value indicator from user input is correctly propagated through the data processing pipeline and by removing an extraneous transformation from the generated code.

Changes

R/main_calculations.R

• Refactored the MSstatsHandleMissing() call in lf_summarization_loop to use explicit named parameters
• Changed missing_symbol parameter from a hardcoded "NA" value to dynamically use qc_input$censInt, ensuring the censored integer parameter is correctly threaded through the function
• The censored_cutoff argument continues to derive from QC_check(qc_input, loadpage_input) but is now passed as a named parameter for improved code clarity
• Lines changed: +7/-3

R/utils.R

• Removed the spurious unique(as.data.frame(data)) transformation from the getDataCode() function
• This eliminates an unnecessary deduplication step in the generated R script code for non-PTM inputs that was not part of the intended data processing pipeline
• Lines changed: +0/-3

Tests

Existing unit tests in tests/testthat/test-main_calculations.R cover the lf_summarization_loop function, including tests that verify the correct summarization function is called based on the summary method selection. The test suite includes tests for both "linear" and "TMP" summary methods.

Tests in tests/testthat/test-utils.R validate that getDataCode() correctly generates character strings for various input configurations and file types.

Coding Guidelines

The changes adhere to the existing codebase conventions. The use of explicit named parameters in function calls improves code readability and reduces the risk of parameter order-related bugs.

[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: 611500e7-cffc-4393-9dd2-a0ed8ebb8e5e

📥 Commits

Reviewing files that changed from the base of the PR and between ba5966d and 8d76f6e.

📒 Files selected for processing (2)

• R/main_calculations.R
• R/utils.R

💤 Files with no reviewable changes (1)

• R/utils.R

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📝 Walkthrough

Walkthrough

This PR refactors missing value handling in the LF summarization pipeline by updating the MSstatsHandleMissing call to use named parameters and input-driven missing symbols, and removes redundant deduplication logic from code generation.

Changes

Summarization and Data Processing Refactor

Layer / File(s)	Summary
MSstatsHandleMissing parameter refactoring R/main_calculations.R	The lf_summarization_loop function refactors the MSstatsHandleMissing invocation to use named parameters and updates the missing-symbol parameter from the constant "NA" to qc_input$censInt, allowing missing value interpretation to be driven by input configuration.

Estimated code review effort

🎯 2 (Simple) | ⏱️ ~8 minutes

Possibly related PRs

• Vitek-Lab/MSstatsShiny#198: Both PRs modify R/main_calculations.R's LF/TMT summarization flow—this PR refactors lf_summarization_loop's MSstatsHandleMissing missing-value handling, while PR #198 changes the LF summarization selection and moderation argument passed to the TMT moderation t-test.

Poem

🐰 Named parameters now align,
No more "NA" cast in stone—
censInt takes the sign,
Dedupe fades when it's not shown,
Clean parameters, code well-defined!

🚥 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 specifically describes the main changes: fixing issue #185 by threading censoredInt correctly and removing an unnecessary unique() call in exported script.
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.

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✨ Finishing Touches

🧪 Generate unit tests (beta)

• Create PR with unit tests
• Commit unit tests in branch MSstatsShiny/work/20260514_censoredint_param_threading

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