Add option to use MS1Quantity for quantifications for Spectronaut

[tonywu1999]

Motivation and Context

Add option to use MS1Quantity for quantifications for Spectronaut. Right now, this is not possible.

Changes

• Enable option to use MS1 quantification from Spectronaut.

Testing

Added unit tests for clean function.

Checklist Before Requesting a Review

• I have read the MSstats contributing guidelines
• My changes generate no new warnings
• Any dependent changes have been merged and published in downstream modules

Summary by CodeRabbit

• New Features

  • Runtime selection and mapping of intensity sources (PeakArea, NormalizedPeakArea, MS1Quantity) so users can choose MS1-level quantification when MS2 is unreliable.

• Documentation

  • Clarified intensity parameter descriptions and anomaly-scoring options, detailing available intensity choices and anomalyModelFeatures requirements.

• Tests

  • Added a unit test validating MS1Quantity intensity handling and error on invalid intensity.

• Chores

  • Removed prior pre-validation of the intensity parameter during input checks.

[coderabbitai]

📝 Walkthrough

Walkthrough

Replaces hard-coded F handling with an intensity_column_mapping resolved at runtime, exposes three intensity options (PeakArea, NormalizedPeakArea, MS1Quantity) in docs and function defaults, updates callers/renames to use resolved column, adds a unit test, and removes an earlier intensity type-check.

Changes

Cohort / File(s)	Summary
Core cleaning & mapping R/clean_Spectronaut.R	Added intensity_column_mapping; resolve selected intensity at runtime; use mapped column for selection and renames instead of paste0("F", intensity); preserves anomaly scoring control flow.
Converter interface R/converters_SpectronauttoMSstatsFormat.R	Made intensity parameter accept vector of allowed values ('PeakArea', 'NormalizedPeakArea', 'MS1Quantity') and updated related docs/signature formatting.
Validation utils R/utils_checks.R	Removed prior explicit intensity type-validation block (intensity is no longer pre-validated there).
Unit tests inst/tinytest/test_clean_Spectronaut.R	Added test exercising MS1Quantity mapping: sets FG.MS1Quantity, runs .cleanRawSpectronaut(intensity='MS1Quantity'), asserts output intensities and error on invalid intensity.
Documentation man/MSstatsClean.Rd, man/SpectronauttoMSstatsFormat.Rd, man/dot-cleanRawSpectronaut.Rd	Expanded intensity descriptions to document three options and clarified calculateAnomalyScores / anomalyModelFeatures behavior; no signature changes in docs beyond parameter text.

Estimated code review effort

🎯 3 (Moderate) | ⏱️ ~20 minutes

Possibly related PRs

• Feature anomaly model #111: Modifies the Spectronaut conversion pipeline (including .cleanRawSpectronaut, SpectronauttoMSstatsFormat, and utils_checks) and appears directly related to anomaly-scoring and intensity handling changes.

Poem

🐰 I mapped the peaks with nimble paws,

From MS2 whispers to MS1 laws,
Three names I learn, one path I choose,
Columns align — no more to lose,
Hoppity clean, the data wows ✨

🚥 Pre-merge checks | ✅ 3

✅ Passed checks (3 passed)

Check name	Status	Explanation
Title check	✅ Passed	The title 'Add option to use MS1Quantity for quantifications for Spectronaut' directly and accurately summarizes the main change in the changeset.
Description check	✅ Passed	The PR description includes all required template sections: Motivation and Context (clear problem statement), Changes (concise bullet point), Testing (mentions unit tests added), and completed Checklist items.
Docstring Coverage	✅ Passed	No functions found in the changed files to evaluate docstring coverage. Skipping docstring coverage check.

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✨ Finishing touches

🧪 Generate unit tests (beta)

• Create PR with unit tests
• Post copyable unit tests in a comment
• Commit unit tests in branch refactor-spec

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No actionable comments were generated in the recent review. 🎉

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[coderabbitai]

Actionable comments posted: 1

🤖 Fix all issues with AI agents

In `@R/clean_Spectronaut.R`:
- Around line 21-26: The code does not validate the intensity argument before
mapping, so intensity_column_mapping[[intensity]] can return NULL and silently
drop the intensity column; update the validation in the function that defines
intensity_column_mapping by ensuring intensity is one of the allowed keys (e.g.
use match.arg(intensity, choices = names(intensity_column_mapping)) or if (!
intensity %in% names(intensity_column_mapping)) stop(...)), then perform the
lookup for intensity_column; additionally, after computing intensity_column
check for NULL and raise a clear error mentioning the accepted options
(referencing intensity_column_mapping and intensity_column).

🧹 Nitpick comments (1)

inst/tinytest/test_clean_Spectronaut.R (1)

1-11: Good coverage of the happy path for MS1Quantity.

The test correctly validates that the MS1Quantity column value flows through to Intensity in the output.

Two suggestions:

1. Consider adding a negative test for an invalid intensity value to ensure a clear error is raised (especially relevant if the validation fix from clean_Spectronaut.R is applied).
2. Consider adding a test that verifies PeakArea still works as expected (regression guard).

,