FracFixR 1.0.0

Initial CRAN Release

This is the first release of FracFixR, a compositional statistical framework for absolute proportion estimation between fractions in RNA sequencing data.

Features

• Core functionality
  • FracFixR(): Main function for fraction correction using NNLS regression
  • DiffPropTest(): Statistical testing for differential proportions between conditions
  • Support for any RNA fractionation protocol (polysome profiling, subcellular localization, etc.)
• Statistical methods
  • Non-negative least squares (NNLS) regression for fraction weight estimation
  • Three test options: GLM (binomial), Logit, and Beta-binomial Wald
  • Automatic estimation of “lost” unrecoverable fraction
  • FDR correction for multiple testing
• Visualization
  • PlotFractions(): Stacked bar plots of fraction proportions
  • PlotComparison(): Enhanced volcano plots for differential results
  • Diagnostic plots for regression quality
• Performance
  • Automatic parallel processing using available CPU cores
  • Efficient handling of large datasets (tested up to 50,000 transcripts)
  • Memory-efficient implementation

Documentation

• Comprehensive function documentation with examples
• Introductory vignette with workflow demonstration
• Detailed README with troubleshooting guide

Testing

• Unit tests covering all major functions
• Validation against synthetic data with known ground truth
• Reproducibility tests ensuring consistent results

Known Limitations

• Requires at least one “Total” sample per condition-replicate combination
• Minimum of 10 transcripts recommended for reliable regression
• Statistical tests require at least 2 replicates per condition

Future Development

We welcome contributions and feedback. Please report issues at: https://github.com/Arnaroo/FracFixR/issues