standardize column names for run for MSstatsAnomalyScores

[tonywu1999]

Motivation and context

• Inconsistent Run column naming from different backends (e.g., Spectronaut) could break run-level filtering, fragment construction, and the merge with run order in MSstatsAnomalyScores.
• Solution: Standardize Run column values early in anomaly input preparation so downstream steps rely on a consistent key.

Detailed changes

• R/utils_anomaly_score.R
  • Standardize input$Run via .standardizeColnames(input$Run) before:
    • Constructing Fragment identifiers.
    • Computing runs = length(unique(input$Run)) for missingness-based fragment filtering.
  • Ensure run_order$Run is standardized via .standardizeColnames(run_order$Run) prior to merging.
  • Merge performed by "Run" relies on standardized keys to prevent dropped rows or misaligned orders.

[coderabbitai]

📝 Walkthrough

Walkthrough

The pull request adds column name standardization to the Spectronaut anomaly input preparation function. A single .standardizeColnames() call is inserted on input$Run before fragment construction and subsequent filtering and merge operations use the normalized column names.

Changes

Column name standardization for anomaly score preparation

Layer / File(s)	Summary
Standardize Run column names before downstream processing R/utils_anomaly_score.R	.prepareSpectronautAnomalyInput() now standardizes column names on input$Run immediately before building fragments and applying run-level filters and merges.

Estimated code review effort

🎯 1 (Trivial) | ⏱️ ~2 minutes

Possibly related PRs

• Vitek-Lab/MSstatsConvert#134: Both PRs standardize the "Run" column in .prepareSpectronautAnomalyInput() to ensure consistent join-key names across downstream fragment construction and merging operations.

Poem

🐰 A tiny line, so clean and small,
Standardizing columns, once and for all!
No more mismatches in the Run,
Spectronaut anomalies—now they're done!

🚥 Pre-merge checks | ✅ 4 | ❌ 1

❌ Failed checks (1 warning)

Check name	Status	Explanation	Resolution
Description check	⚠️ Warning	The pull request description is completely empty. The author did not fill in the template with any motivation, changes, testing details, or checklist completion.	Add a comprehensive PR description including: motivation and context for standardizing column names, detailed list of changes made to the function, description of any tests added or modified, and completion of the pre-review checklist.

✅ Passed checks (4 passed)

Check name	Status	Explanation
Title check	✅ Passed	The title clearly and specifically describes the main change: standardizing column names for the 'run' variable in MSstatsAnomalyScores functionality.
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 docstrings

• Create stacked PR
• Commit on current branch

🧪 Generate unit tests (beta)

• Create PR with unit tests
• Commit unit tests in branch col-names

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