/TWAS_vs_coloc

Repository for TWAS vs. coloc paper

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Analyzing and Reconciling Colocalization and Transcriptome-wide Association Studies from the Perspective of Inferential Reproducibility

This repo documents the data analysis and simulation studies performed in the manuscript "Analyzing and Reconciling Colocalization and Transcriptome-wide Association Studies from the Perspective of Inferential Reproducibility". The manuscript is available here.

Software Implementation

The locus-level colocalization method described in the manuscript is implemented in the software package fastENLOC, version 2.

Simulation Studies

We describe two different simulation studies:

  1. Illustrating the LD hitchhiking effect in TWAS scan analysis. The code and main results are included in the directory LD_hitchhiking
  2. Assessing the empirical power of the proposed locus-level colocalization analysis. The corresponding code, results, and descriptions can be found in the directory locus_coloc_sim

GWAS and GTEx Data Analysis

The relevant data, analysis code, and descriptions are included in the directory gtex_gwas_analysis.

References

  • Hukku, A., Sampson, M.G., Luca, F., Pique-Regi, R. and Wen, X., 2021. Analyzing and Reconciling Colocalization and Transcriptome-wide Association Studies from the Perspective of Inferential Reproducibility. BioRxiv doi:10.1101/2021.10.29.466468.