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eQTpLot: a user-friendly R package for the visualization of colocalization between eQTL and GWAS signals
Theodore G Drivas1,2, Anastasia Lucas3, Marylyn D Ritchie3,4
1Division of Human Genetics, Children's Hospital of Philadelphia, Philadelphia, PA, USA. theodore.drivas@pennmedicine.upenn.edu.
The R package eQTpLot visualizes colocalization between expression quantitative trait loci (eQTL) and genome-wide association study (GWAS) results. This tool aids researchers in understanding gene expression
Area of Science:
- Genomics
- Statistical Genetics
- Bioinformatics
Background:
- Genomic studies increasingly integrate expression quantitative trait loci (eQTL) data.
- Limited tools exist for visualizing colocalization between eQTL and genome-wide association study (GWAS) results.
- Existing tools lack comprehensive analysis options and integrated visualization of eQTL and GWAS data.
Purpose of the Study:
- To develop an intuitive R package for visualizing colocalization between eQTL and GWAS results.
- To provide a user-friendly tool for exploring the relationship between gene expression and trait associations.
Main Methods:
- Developed the R package eQTpLot.
- Input includes standard GWAS and cis-eQTL summary statistics, and optional pairwise LD information.
- Generates customizable plots for colocalization, correlation, and enrichment analysis.
Main Results:
- eQTpLot generates plots illustrating eQTL-GWAS colocalization, correlation of p-values, eQTL enrichment, LD landscape, and direction of effect.
- Provides a clear and comprehensive visualization of the interplay between gene expression and trait associations.
- Facilitates a deeper understanding of genetic architecture underlying complex traits.
Conclusions:
- eQTpLot offers a unique, user-friendly, and intuitive method for visualizing eQTL and GWAS signal colocalization.
- Incorporates novel features not available in other eQTL visualization software.
- A valuable tool for researchers needing convenient and customizable visualization of eQTL-GWAS data.
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