EntrapmentAnalyses.jl

EntrapmentAnalyses.jl is a Julia package for entrapment-based false discovery rate (FDR) analysis in proteomics data. It implements both combined and paired empirical FDR (EFDR) methods for precursor-level and protein-level analyses.

Features

• Data Loading: Support for Parquet and TSV file formats
• EFDR Calculation: Both combined and paired empirical FDR methods
• Protein Analysis: Protein-level rollup and per-run analysis
• Visualization: Automated generation of EFDR plots and reports
• Performance: Optimized for large-scale proteomics datasets

Installation

Navigate to the EntrapmentAnalyses directory. Use ] to enter Pkg mode.

(@v1.11) pkg> activate .
  Activating project at `~/Projects/EntrapmentAnalysesJmod/EntrapmentAnalyses`

julia> using Revise, EntrapmentAnalyses
Precompiling EntrapmentAnalyses...
  1 dependency successfully precompiled in 6 seconds. 273 already precompiled.

Quick Start

using EntrapmentAnalyses

# Run precursor-level EFDR analysis
results = run_efdr_analysis(
    ["data/psm_results.parquet"],
    "data/spectral_library.tsv";
    output_dir="output"
)

# Run protein-level EFDR analysis
protein_results = run_protein_efdr_analysis(
    ["data/psm_results.parquet"],
    "data/spectral_library.tsv";
    output_dir="output"
)

Documentation Contents

• User Guide
• • Installation
  • Input Data Requirements
  • Basic Usage
  • Advanced Options
  • Working with Results
  • Troubleshooting
  • Best Practices
• Tutorial
• • Setup
  • Example 1: Basic Precursor-Level Analysis
  • Example 2: Multi-Run Analysis
  • Example 3: Protein-Level Analysis
  • Example 4: Custom Analysis Pipeline
  • Example 5: Handling Special Cases
  • Example 6: Batch Processing
  • Tips and Best Practices
  • Next Steps
• API Reference
• • Main API Functions
  • Data Loading
  • Analysis Functions
  • EFDR Calculation
  • Q-value Calculation
  • Pairing System
  • Visualization
  • Type Definitions
  • Index

Package Overview

EntrapmentAnalyses.jl provides a comprehensive toolkit for analyzing entrapment-based FDR in proteomics experiments. The package is designed to handle the complete workflow from data loading through analysis to visualization.

Key Components

1. Data Loading: Robust handling of various input formats with automatic missing value management
2. Pairing System: Sophisticated peptide pairing that respects both file and plex boundaries
3. EFDR Methods: Implementation of both combined and paired EFDR calculations
4. Protein Analysis: Tools for protein-level rollup and per-run analysis
5. Visualization: Automated plot generation with customizable parameters

Workflow

1. Load PSM results and spectral library data
2. Compute peptide pairings with plex-aware complement scoring
3. Calculate per-file q-values
4. Perform EFDR analysis (combined and/or paired)
5. Generate visualizations and reports
6. Optional: Perform protein-level analysis

Getting Help

• Check the User Guide for detailed usage instructions
• Follow the Tutorial for a step-by-step walkthrough
• Consult the API Reference for function documentation
• Report issues on GitHub