edge-gwas

Contents:

  • Installation Guide
    • System Requirements
    • Quick Installation
    • Virtual Environment (Recommended)
    • Optional Dependencies
    • Upgrading from v0.1.0
    • Troubleshooting
    • See Also
  • Quick Start Guide
    • Overview
    • EDGE Methodology
    • Complete Workflow Example
    • Step-by-Step Guide
      • 1. Load Data
      • 2. Quality Control
      • 3. Population Structure Control
      • 4. Split Data
      • 5. Run EDGE Analysis
      • 6. Visualize Results
      • 7. Interpret Results
    • Output Files
    • Best Practices
      • Quality Control
      • Covariates
      • Data Splitting
      • Performance
    • Advanced Features
      • Cross-Validation
      • Compare with Additive GWAS
      • Outcome Transformations
    • Troubleshooting
    • Quick Reference
    • See Also
  • Statistical Model
    • Overview
    • Regression Models
    • Encoding Parameter
    • Outcome Types
    • Optimization Methods
    • Outcome Transformations
    • Statistical Testing
    • Quality Control
    • Best Practices
    • 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 v0.1.2 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
  • API Reference
    • Quick Function Finder
    • Core Analysis
      • EDGEAnalysis
        • EDGEAnalysis.calculate_alpha()
        • EDGEAnalysis.apply_alpha()
        • EDGEAnalysis.run_full_analysis()
        • EDGEAnalysis.get_skipped_snps()
    • Data Loading
      • load_plink_data()
      • load_pgen_data()
      • load_vcf_data()
      • load_bgen_data()
      • prepare_phenotype_data()
      • download_test_files()
    • Data Validation
      • validate_genotype_df()
      • validate_and_fix_encoding()
      • validate_phenotype_df()
      • validate_and_align_data()
    • Quality Control
      • filter_genotype_data()
      • filter_variants_by_maf()
      • filter_variants_by_missing()
      • filter_samples_by_call_rate()
      • calculate_hwe_pvalues()
      • filter_variants_by_hwe()
      • check_case_control_balance()
    • Population Structure Control
      • calculate_grm_gcta()
      • load_grm_gcta()
      • calculate_pca_sklearn()
      • calculate_pca_plink()
      • calculate_pca_pcair()
      • attach_pcs_to_phenotype()
      • get_pc_covariate_list()
      • identify_related_samples()
      • filter_related_samples()
    • Data Preparation
      • stratified_train_test_split()
      • impute_covariates()
    • Standard GWAS
      • standard_gwas()
      • additive_gwas()
      • cross_validated_edge_analysis()
    • Visualization
      • manhattan_plot()
      • qq_plot()
      • plot_alpha_distribution()
    • Input/Output
      • save_results()
      • load_alpha_values()
      • format_gwas_output_for_locuszoom()
      • save_for_locuszoom()
      • validate_locuszoom_format()
      • create_summary_report()
    • Function Index
      • 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
  • Citation
    • Primary Citation
    • BibTeX Entry
    • Acknowledgments
    • Contact for Citation Questions
    • See Also
  • Changelog
    • Version 0.1.2 (2026-02-10)
      • Fixed
      • Changed
    • Version 0.1.1 (2025-12-27)
      • 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
  • 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
edge-gwas
  • Search

© Copyright 2025, edge-gwas Contributors.

Built with Sphinx using a theme provided by Read the Docs.