feat(diann): Add support for DIANN 2.0

[tonywu1999]

Motivation and Context

https://groups.google.com/g/msstats/c/NoBiovXEiiY

Changes

• Add support for DIANN's new output format
• Add example for parquet data input

Testing

• Added unit tests

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

Summary by CodeRabbit

• New Features

  • Added support for an "auto" option in quantification settings to handle DIANN 2.0 data, automatically combining fragment intensity columns for easier processing.

• Documentation

  • Updated documentation to describe the new "auto" quantification option and provide clearer usage instructions and examples for DIANN 2.0 data.

• Tests

  • Added new test coverage for DIANN 2.0 data format using the "auto" quantification option to ensure accurate processing and output consistency.

[Copilot]

Pull Request Overview

Adds support for DIANN 2.0 by introducing an auto mode for quantificationColumn to collapse multiple fragment columns into a single intensity column.

• Extend documentation across functions to describe the new auto option.
• Implement logic in clean_DIANN.R to detect and merge fragment columns when quantificationColumn = "auto".
• Update examples to reference the auto setting.

Reviewed Changes

Copilot reviewed 5 out of 5 changed files in this pull request and generated 1 comment.

Show a summary per file

File	Description
man/dot-cleanRawDIANN.Rd	Document new auto option for quantificationColumn.
man/MSstatsClean.Rd	Document new auto option for quantificationColumn.
man/DIANNtoMSstatsFormat.Rd	Document new auto option and update example comment.
R/converters_DIANNtoMSstatsFormat.R	Document new auto option in roxygen and update example.
R/clean_DIANN.R	Add auto-detection and collapse of fragment columns.

Comments suppressed due to low confidence (3)

man/dot-cleanRawDIANN.Rd:18

• Wrap code elements such as 'FragmentQuantCorrected', 'FragmentQuantRaw', and 'auto' in \code{} for proper Rd formatting and consistent styling.

\item{quantificationColumn}{Use 'FragmentQuantCorrected'(default) column for quantified intensities.

R/clean_DIANN.R:16

• Add unit tests to cover the new 'auto' behavior, including scenarios with zero fragment columns and multiple fragment columns to ensure correct merging and error handling.

  if (quantificationColumn == "auto") {

man/DIANNtoMSstatsFormat.Rd:83

• [nitpick] Rather than only noting the 'auto' setting in a comment, include a full example call (e.g., DIANNtoMSstatsFormat(file, annotation, quantificationColumn = 'auto')) to demonstrate how to use it.

# For DIANN 2.0, set quantificationColumn = 'auto'

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