fix(spectronaut): Enable Fraction column to be processed

[tonywu1999]

Motivation and Context

Spectronaut experimental files include an RFraction column that represents sample fractionation information, but the .cleanRawSpectronaut() function was not processing this column. This fix enables the function to properly recognize, extract, and rename the RFraction column from the input data to align with the MSstats output schema, where it is expected as the Fraction field.

Changes

• Column Selection Enhancement: Added "RFraction" to the list of columns selected from the raw Spectronaut input (line 32 in clean_Spectronaut.R)

• Column Renaming Mapping: Updated the data.table::setnames() call to include a mapping from "RFraction" (source) to "Fraction" (output schema name) (line 44-47 in clean_Spectronaut.R)

• Graceful Handling of Missing Column: Added skip_absent = TRUE parameter to the setnames() function to ensure the function continues to work correctly when the RFraction column is absent from the input, maintaining backward compatibility with existing Spectronaut files that don't include fractionation information

Unit Tests

• Backward Compatibility Test: Verifies that when R.Fraction is absent from the input data, no Fraction column is added to the output, preserving existing behavior (lines 12-13 in test_clean_Spectronaut.R)

• RFraction Transfer Test: Confirms that when R.Fraction is present in the input, it is properly transferred to the output as the Fraction column with the correct values (lines 15-25 in test_clean_Spectronaut.R)

• Column Naming Verification: Asserts that the intermediate column name RFraction does not appear in the output (only the renamed Fraction column is present), ensuring correct schema compliance (line 24 in test_clean_Spectronaut.R)

Code Guidelines

No violations identified. The implementation follows the existing code patterns in the repository, uses appropriate R/data.table idioms, and maintains consistency with how other optional columns are handled in the cleaning pipeline.

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ℹ️ Review info

⚙️ Run configuration

Configuration used: Organization UI

Review profile: CHILL

Plan: Pro

Run ID: e191c630-8a84-4ab2-83a0-85a0d2155ff5

📥 Commits

Reviewing files that changed from the base of the PR and between 846c142 and bca444c.

📒 Files selected for processing (2)

• R/clean_Spectronaut.R
• inst/tinytest/test_clean_Spectronaut.R

📝 Walkthrough

Walkthrough

This PR extends Spectronaut data cleaning to include the RFraction column. The function now selects RFraction from raw input and renames it to Fraction in the cleaned output, with tests covering both the absence and presence of fraction data.

Changes

Fraction column support in Spectronaut cleaning

Layer / File(s)	Summary
RFraction column selection and output renaming R/clean_Spectronaut.R	The cols vector now includes RFraction, and the data.table::setnames mapping is updated to rename RFraction to Fraction in the output schema.
Fraction column test coverage inst/tinytest/test_clean_Spectronaut.R	Tests verify that no Fraction column is added when R.Fraction is absent, and that R.Fraction is successfully renamed to Fraction when present in the input.

Estimated code review effort

🎯 1 (Trivial) | ⏱️ ~5 minutes

Poem

🐰 A fraction of a change, so clean and bright,
Where RFraction becomes Fraction in the light,
The Spectronaut pipeline flows on true,
With tests to prove the old and the new! ✨

🚥 Pre-merge checks | ✅ 4 | ❌ 1

❌ Failed checks (1 warning)

Check name	Status	Explanation	Resolution
Description check	⚠️ Warning	Pull request description is incomplete. Required sections lack substantive content: motivation/context is a placeholder, changes list is empty, and testing section has no details.	Add motivation and context explaining why fraction column processing is needed. Provide detailed bullet points of changes and describe the unit tests added to verify the implementation.

✅ Passed checks (4 passed)

Check name	Status	Explanation
Title check	✅ Passed	The title accurately describes the main change: enabling Spectronaut's Fraction column processing in the cleaning function.
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 fix-fractions

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