Validation datasets, code, and plots for the Archipelago method.

Archipelago Validation This directory contains validation studies for the Archipelago method, a framework for integrating single-variant GWAS and variant set association test (VSAT) statistics. . ├── README.md ├── data │ ├── 1kg │ ├── ukbb │ └── ukbb_phewas ├── output │ ├── archipelago_plot_1kgeas.png │ ├── archipelago_plot_1kgeas_enriched_variant_frequencies.png │ ├── archipelago_plot_ukbb_PheWAS.png │ ├── archipelago_plot_ukbb_full.png │ ├── archipelago_plot_ukbb_subset.png │ ├── archipelago_plot_vsat_raw_1kgeas.png │ └── archipelago_plot_vsat_raw_ukbb.png └── src ├── 1kg_archipelago.R ├── ukbb_archipelago_v0.R └── ukbb_phewas_archipelago_v0.R Input The manuscript included three validation datasets: data/1kg/ — 1000 Genomes Project (East Asian samples) read GWAS trait and simulated pathway-level trait. data/panukbb/ — Pan-UK Biobank (platelet distribution width, DeepRVAT) real GWAS and gene-level trait. data/ukbb_wgs/ — UK Biobank WGS (UTR collapsing PheWAS) real GWAS and gene-level trait. Each data subdirectory contains its own README with workflow details, source data, and outputs used in the validation studies. Output The `output/` folder contains final plots from the three validation studies: | Study | Archipelago Plot | VSAT Raw Plot | |------------|----------------------------------------|-----------------------------------------------| | 1KG | `archipelago_plot_1kgeas.png` | `archipelago_plot_vsat_raw_1kgeas.png` | | Pan-UKBB | `archipelago_plot_ukbb_full.png` | `archipelago_plot_vsat_raw_ukbb.png` | | UKBB WGS | `archipelago_plot_ukbb_wgs.png` | `archipelago_plot_vsat_raw_ukbb_wgs.png` | The enriched variant frequency summary for 1KG is also available:- `archipelago_plot_1kgeas_enriched_variant_frequencies.png` A downsampled version of the UKBB plot for display is provided:- `archipelago_plot_ukbb_subset.png` Scripts Reproducible plotting scripts are available under `src/`: `1kg_archipelago.R` `panukbb_archipelago_v0.R` `ukbb_wgs_archipelago_v0.R` These scripts prepare the input data and run the final integrated Archipelago visualisations per study Citation For methodology and results, see: Archipelago method for variant set association test statisticsDylan Lawless, et al. medRxiv 2025.03.17.25324111 https://doi.org/10.1101/2025.03.17.25324111