PostHoc

User guide

  • Installation
    • Requirements
    • Install from source
    • Optional dependency sets
    • Verifying the install
    • GPU support
    • Next steps
  • Quickstart
    • Prerequisites
    • 1. Simulate a phenotype with known causal SNPs
    • 2. Sanity-check with a linear baseline
    • 3. Train an MLP and compute SNP attributions
    • 4. Run PAL for robust, multi-model locus discovery
    • 5. Compare against ground truth
    • Next steps
  • Input data formats
    • Genotype input (--pfile)
    • Phenotype input (--pheno)
    • Covariate input (--covar)
    • Sample alignment
    • Quality control filters
    • Output formats
  • Output formats
    • simulate-pheno outputs
    • attribute output (.glm-style TSV)
    • pal output (TSV)
  • Concepts and methodology
    • The overall approach
    • The MLP model
    • Integrated Gradients attribution
    • PAL and AMAS
    • Null model and significance testing
    • Practical implications for choosing options
    • Relationship to prior work

Reference

  • Command-line reference
    • posthoc
    • simulate-pheno
      • posthoc simulate-pheno
      • Effect term encoding
      • Outputs
    • baseline
      • posthoc baseline
      • Behavior notes
      • Example output
    • attribute
      • posthoc attribute
      • Behavior notes
      • Example
    • pal
      • posthoc pal
      • Behavior notes
      • Example
  • Python API reference
    • posthoc.io
      • Genotype reader
      • Phenotype and covariate reader
      • Writers
    • posthoc.qc
      • QCResult
      • compute_maf()
      • compute_missing_rate()
      • filter_maf()
      • filter_geno()
      • indep_pairwise()
      • apply_ld_pruning()
      • run_qc()
    • posthoc.models
      • Base classes and configuration
      • MLP
      • Training utilities
    • posthoc.attribution
      • Integrated Gradients
      • PAL / AMAS
      • Significance testing
    • posthoc.simulation
      • PhenotypeModel
      • SimulationResult
      • simulate_phenotype()
      • simulate()
    • Package overview

Project

  • Development
    • Setup
    • Running tests
    • Project layout
    • Building the documentation locally
    • Coding conventions
    • Contributing
PostHoc
  • Search

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