Comprehensive Refactoring Plan for artMS R Package Modernization

[biodavidjm]

This R package provides proteomics data analysis workflows with four core functional modules:

• Quality control (QC) functions for proteomics data
• Relative quantification using MSstats integration
• Downstream statistical analysis (enrichment, clustering, PCA, visualization)
• Export utilities for external tools (SAINTq, SAINTexpress, Photon, Phosfate)

Refactoring Objectives:

Provide a detailed, prioritized refactoring plan addressing:

Code Modernization:

• Update to modern R practices (tidyverse compatibility, pipe operators, tidy evaluation)
• Replace deprecated functions and dependencies
• Implement consistent coding style (tidyverse style guide)
• Add type checking and input validation

Package Structure:

• Reorganize functions into logical modules matching the four core areas
• Identify and eliminate code duplication
• Separate plotting/visualization into dedicated functions
• Modularize export functions for each external tool

Dependencies:

• Audit current dependencies for relevance and maintenance status
• Update MSstats integration to latest API
• Minimize dependency footprint where possible
• Document version requirements

Testing & Documentation:

• Add unit tests (testthat) for each functional module
• Create example datasets for testing
• Write comprehensive vignettes for each workflow
• Improve function documentation (roxygen2)
• Add lifecycle badges for function maturity

Performance:

• Identify computational bottlenecks
• Implement parallel processing where appropriate
• Optimize memory usage for large datasets

User Experience:

• Standardize function naming conventions
• Improve error messages and warnings
• Add progress indicators for long-running operations
• Create consistent return object structures

Backwards Compatibility:

• Strategy for deprecated function migration
• Version migration guide for existing users

Deliverable Format:

• Pased implementation plan (Phase 1: critical updates, Phase 2: enhancements, Phase 3: new features)
• Specific file structure recommendations
• Priority ranking for each task
• Estimated effort/complexity for major refactoring tasks
• Breaking changes documentation strategy