edge-gwas

Contents:

  • Installation Guide
    • System Requirements
    • Dependencies
    • Quick Installation
    • Installation from GitHub
    • Installation from Source
    • Virtual Environment Setup
    • External Tools Installation (NEW in v0.1.1)
    • Verify Installation
    • Supported File Formats
    • Upgrading from v0.1.0
    • Troubleshooting
      • Common Issues
    • Platform-Specific Notes
    • Development Installation
    • Docker Installation (Optional)
    • Singularity/Apptainer (for HPC)
    • Testing Your Installation
    • Installation Checklist
      • Minimum Installation (Core Only)
      • Recommended Installation (Full Features)
    • Configuration
    • Uninstallation
    • Getting Help
    • Next Steps
    • See Also
  • Quick Start Guide
    • Minimal Example
    • Complete Example with v0.1.1 Features
    • Step-by-Step Workflow
      • 1. Install and Setup
      • 2. Import Packages
      • 3. Load Data
      • 4. Quality Control
      • 5. Population Structure Control (NEW in v0.1.1)
      • 6. Initialize EDGE Analysis
      • 7. Split Data
      • 8. Run EDGE Analysis
      • 9. Examine Results
      • 10. Visualize Results
    • Understanding the Output
      • Alpha Values DataFrame
      • GWAS Results DataFrame
      • Interpreting Alpha Values
    • Quick Recipes
      • Recipe 1: Continuous Trait with Transformation
      • Recipe 2: Analysis with Related Samples
      • Recipe 3: Compare EDGE with Additive Model
      • Recipe 4: Cross-Validation
      • Recipe 5: Multi-Format Data Loading
    • Common Workflow Patterns
      • Pattern 1: Basic Case-Control Study
      • Pattern 2: Quantitative Trait Study
      • Pattern 3: Biobank-Scale Analysis
    • Troubleshooting Quick Fixes
    • What’s New in v0.1.1?
    • See Also
  • User Guide
    • Overview
    • EDGE Methodology
    • Complete Workflow
      • 1. Load Data
      • 2. Quality Control
      • 3. Population Structure Control (NEW in v0.1.1)
      • 4. Split Data
      • 5. Run EDGE Analysis
      • 6. Interpret Results
      • 7. Visualize
    • File Formats
    • Best Practices
      • Quality Control
      • Covariates
      • Data Splitting
      • Performance
    • Advanced Features (v0.1.1)
      • Cross-Validation
      • Compare with Additive GWAS
      • Population Structure Options
      • Outcome Transformations
    • Troubleshooting
      • Common Issues
    • Quick Reference
    • See Also
  • API Reference
    • Core Module
    • EDGEAnalysis Class
      • Methods
        • calculate_alpha()
        • apply_alpha()
        • run_full_analysis()
        • get_skipped_snps()
    • Utilities Module
    • load_plink_data()
    • load_pgen_data()
    • load_vcf_data()
    • load_bgen_data()
    • prepare_phenotype_data()
    • filter_genotype_data()
    • validate_and_align_data()
    • validate_genotype_df()
    • validate_and_fix_encoding()
    • Visualization Module
    • I/O Handlers Module
    • Data Structures
    • Constants and Defaults
    • Exceptions
    • Version Information
    • Command-Line Tools (NEW in v0.1.1)
    • Function Reference Summary
    • Complete Workflow Example
    • Migration Guide (v0.1.0 → v0.1.1)
    • Function Index
    • Quick Function Finder
    • See Also
  • Statistical Model
    • Overview
    • Regression Model
      • Stage 1: Codominant Model (Training Data)
    • Encoding Parameter
      • Stage 2: EDGE-Encoded Model (Test Data)
    • Interpretation of Alpha
    • Two-Stage Analysis
      • Why Two Stages?
      • Stage 1: Calculate Alpha (Training Data)
      • Stage 2: Apply Alpha (Test Data)
    • Outcome Types
      • Binary Outcomes (Logistic Regression)
      • Quantitative Outcomes (Linear Regression)
    • Optimization Methods
      • Available Algorithms
      • Algorithm Details
      • Usage Example
      • Choosing an Optimization Method
      • Convergence Diagnostics
    • Outcome Transformations
      • Available Transformations
      • Log Transformation
      • Inverse Normal Transformation (INT)
      • Rank-Based Inverse Normal Transformation (RINT)
      • Choosing a Transformation
      • Effect Size Interpretation After Transformation
      • Transformation Diagnostics
    • Statistical Testing
      • Hypothesis Testing
      • P-value Calculation
      • Multiple Testing Correction
      • Genomic Inflation Factor
    • Quality Control Considerations
      • Minor Allele Frequency (MAF)
      • Hardy-Weinberg Equilibrium (HWE)
      • Missingness
      • Population Structure
    • Sample Size Considerations
      • Minimum Sample Size
      • Power Calculations
    • Comparison with Other Methods
      • EDGE vs. Standard Additive GWAS
      • EDGE vs. Genotypic Model
      • EDGE vs. Cochran-Armitage Trend Test
    • Practical Considerations
      • When to Use EDGE
      • Recommended Workflow
      • Computational Complexity
    • Implementation Details
      • Software Implementation
      • Convergence Issues
    • Extensions and Future Directions
      • Planned Features (v0.2.0+)
      • Research Directions
    • Limitations
      • Current Limitations
      • Statistical Assumptions
    • Validation Studies
      • Simulation Studies
      • Real Data Applications
      • Method Comparison Studies
    • Mathematical Proofs
      • Unbiased p-values (Sketch)
      • Consistency of α (Sketch)
      • Convergence of Optimization Methods
    • Glossary of Terms
    • Best Practices Summary
      • Data Preparation
      • Parameter Selection
      • Result Interpretation
      • Appendix A: Optimization Method Details
    • See Also
  • Example Workflows
    • Example 1: Basic Binary Outcome Analysis with PCA
    • Example 2: Quantitative Trait with Outcome Transformation
    • Example 3: Analysis with GRM for Related Samples
    • Example 4: Multi-Format Data Loading
    • Example 5: Comprehensive Quality Control Pipeline
    • Example 6: Comparing EDGE with Additive GWAS
    • Example 7: Cross-Validation for Model Stability
    • Example 8: Complete Analysis with All v0.1.1 Features
    • Example 9: Multi-Chromosome Genome-Wide Analysis
    • Example 10: Batch Processing for Very Large Datasets
    • Example 11: Using Pre-Calculated Alpha Values
    • Example 12: Detailed Alpha Interpretation and Reporting
    • Tips and Best Practices
      • Data Preparation
      • Quality Control Best Practices
      • Analysis Strategy
      • Performance Optimization
      • Interpretation Guidelines
      • Common Pitfalls to Avoid
      • Troubleshooting Common Issues
    • See Also
  • Visualization Guide
    • Built-in Visualization Functions
      • Manhattan Plot
        • Basic Usage
        • Advanced Options
        • Multiple Chromosomes
      • QQ Plot
        • Basic Usage
        • Advanced Options
      • Alpha Distribution Plot
        • Basic Usage
        • Advanced Options
    • Custom Visualizations
      • Regional Association Plot
      • Alpha vs Effect Size Plot
      • Forest Plot for Top Hits
      • Comparing Multiple Analyses
    • Interactive Plots with Plotly
      • Volcano Plot
      • Multi-Panel Summary Figure
    • Plotting Tips
      • Color Schemes
      • Figure Resolution
      • Font Sizes
      • Exporting Plots
    • See Also
  • Changelog
    • Version 0.1.1 (2025-12-25) - Current Release
      • Added
      • Changed
      • Migration from v0.1.0
      • Bug Fixes
    • Version 0.1.0 (2025-12-24)
      • Added
      • Dependencies
    • Version 0.0.0 (2024-04-02) - Legacy
    • Version History Summary
    • See Also
  • Citation
    • Primary Citation
    • BibTeX Entry
    • Related Publications
    • Acknowledgments
    • Contact for Citation Questions
    • See Also
  • Troubleshooting Guide
    • Common Issues and Solutions
      • Common Errors and Solutions
    • Error 1: “ValueError: No common samples found between analysis data and GRM”
    • Error 2: “LinAlgError: Matrix is singular”
    • Error 3: “ConvergenceWarning: Maximum iterations reached”
    • Error 4: “ValueError: Log transformation requires all positive values”
    • Error 5: “KeyError: ‘variant_id’ not found”
    • Error 6: “MemoryError: Unable to allocate array”
    • Error 7: “RuntimeWarning: invalid value encountered in divide”
      • Performance Optimization Tips
    • Speed Optimization
    • Memory Optimization
    • Accuracy Optimization
      • Reproducibility Best Practices
    • Setting Random Seeds
    • Version Control
    • Parameter Documentation
    • Appendix A: Troubleshooting Decision Tree
      • See Also
  • Frequently Asked Questions (FAQ)
    • General Questions
    • Technical Questions
    • Interpretation Questions
    • Practical Implementation Questions
      • See Also
  • Advanced Topics for Further Updates
    • Extensions and Future Directions
      • Planned Features
      • Research Directions
    • Advanced Topics
      • Cross-Validation for Alpha Estimation
      • Meta-Analysis of EDGE Results
      • Conditional Analysis
      • Gene-Based Testing (Future Feature Preview)
      • Interaction Effects
      • Stratified Analysis
      • Polygenic Risk Scores with EDGE
      • Sensitivity Analyses
    • Integration with Other Tools
      • LD Score Regression
      • Fine-Mapping
      • Colocalization Analysis
      • Pathway Enrichment
    • Visualization Examples
      • Alpha Distribution Plot
      • Manhattan Plot with Alpha Coloring
      • QQ Plot Comparison
      • Regional Association Plot
      • Effect Size Comparison Plot
      • Convergence Diagnostic Plot
      • Power Analysis Visualization
      • Simulation Code
      • Sample Size Calculations
      • Useful Helper Functions
    • See Also
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