Stability and Fine-Mapping

This repository contains data and scripts for the following paper:

Aw, A.J., Jin, L.C., Ioannidis, N.M., and Song, Y.S. (2023+) "The impact of stability considerations on genetic fine-mapping"

Fine-mapping results

Results are stored under data/results_with_moderators.

For convenience, csv files with both raw and Benjamini-Hochberg-adjusted p-values are also stored under data/results_with_moderators/p_values.

Summary data files

Summary files containing the 378 functional annotations associated with each fine-mapped variant (stable or top) are stored under data/all_func_annots. We recommend directly working with these files to reproduce our findings and figures.

Generating figures in paper

Code for generating figures is stored under scripts.

# Command for Executing Script
Rscript generate_paper_figs.R

Shiny App

Open-source code for building and deploying our Shiny application is under ShinyApp.

Running PICS2

Standalone code for running PICS2 is stored under scripts, along with example data. The example data uses gene expression of PRKAA2 (ENSG00000162409.6), which is transcribed in Chromosome 1.

# Command for Executing Script - RUN AFTER UNZIPPING toy-data/genotype_array.csv.zip
# Internal functions can also be copied and used elsewhere; see R script for details
Rscript runPICS2.R 500 3 toy-data/genotype_array.csv toy-data/phenotype_vector.txt toy-data/snp_metadata.txt toy-data/sample_metadata.txt toy-data/gene_tss_metadata.txt toy-data/covars_array.csv toy-results/