Toxicant GWAS Manuscript

This repository contains all code and data needed to reproduce the analyses and figures from the manuscript "Natural variation suggests candidate genes underlying Caenorhabditis elegans susceptibility to diverse toxicants"

Getting Started

1. Clone the Repository

git clone https://github.com/AndersenLab/ToxinGWAS_Manuscript.git
cd ToxinGWAS_Manuscript

2. Render the Project

# Render the entire project
quarto render

This will:

1. Decompress pre-computed GWAS mapping results (~6 GB)
2. Process raw data to generate all intermediate data files
3. Generate all manuscript figures and tables

Project Structure

• analysis/ - Data processing and analysis scripts
• paper/ - Figure and table generation scripts for the manuscript
• data/raw/ - Raw input data
• data/processed/ - Intermediate processed data
• bin/ - Utility functions and helper scripts
• _products/ - Rendered outputs from analysis/ and paper/ scripts
• figures/ - Generated figures for the manuscript
• tables/ - Generated tables for the manuscript

Analysis Pipeline

The analysis scripts in analysis/ are executed in the following order (as specified in _quarto.yml):

1. Data Processing

   • nemascan_pipeline_documentation.qmd
   • decompress_nemascan_output.qmd
   • organize_tox_metadata.qmd
   • trait_generate_mapping_inputs.qmd

2. Phenotype Analysis

   • organize_strain_means.qmd
   • organize_strain_outliers.qmd
   • calculate_phenotype_correlations.qmd

3. GWAS and Interval Analysis

   • calculate_enrich_each_interval.qmd
   • interval_overlap_identification.qmd
   • hdr_summarize_strain.qmd
   • hdr_calculate_region_overlaps.qmd
   • rank_regions.qmd

4. Candidate Gene Analysis

   • candidate_gene_identification.qmd
   • candidate_gene_GO.qmd
   • candidate_gene_effects.qmd
   • candidate_gene_organization.qmd
   • candidate_gene_orthologs.qmd

5. Semantic Similarity Analysis

   • semantic_similarity_all_genes.qmd
   • semantic_similarity_candidate_genes.qmd

6. Supplementary Materials

   • aggregate_supplementary_tables.qmd

Paper Figures and Tables

The figure and table generation scripts in paper/ are executed after the analysis scripts, as specified in _quarto.yml. These scripts generate all figures and tables used in the manuscript.

products/ Directory

The _products/ directory contains all rendered outputs from the analysis and paper scripts. After running quarto render, you can find:

• Processed data files in _products/analysis/
• Manuscript figures in _products/paper/
• Index file at _products/index.html for easy navigation of all outputs.

Pre-computed GWAS Results

The GWAS mapping results (data/processed/20231116_Analysis_NemaScan/) were generated using the NemaScan pipeline and are provided pre-computed due to computational requirements.

For detailed information about how these results were generated, see the rendered documentation at _products/analysis/nemascan_pipeline_documentation.html after running quarto render, or view the source at analysis/nemascan_pipeline_documentation.qmd.