GitHub - borangao/Logica (original) (raw)

Logica

A likelihood framework for cross-ancestry local genetic correlation estimation using summary statistics (Logica)

Logica (LOcal GenetIc Correlation across Ancestries), a new method specifically designed to estimate local genetic correlations across ancestries. Logica employs a bivariate linear mixed model that explicitly accounts for diverse LD patterns across ancestries, operates on GWAS summary statistics, and utilizes a maximum likelihood framework for robust inference. Logica is implemented as an open-source R package, freely available at Zhou lab.

Installation

To install the latest version of the Logica package from GitHub, run the following code in R:

library(devtools) install_github("borangao/Logica")

This command should automatically install all required packages if they are not installed already.

Quick Start

See Tutorial for detailed documentation and examples. We’re developing local genetic correlation methods for admixed individuals; a beta implementation here

Issues

All feedback, bug reports and suggestions are warmly welcomed! Please contact me at gao824@purdue.edu. Please make sure to raise issues with a detailed and reproducible exmple and also please provide the output of your sessionInfo() in R!

How to cite Logica

Boran Gao, Zheng Li, Xiang Zhou. Logica: A likelihood framework for cross-ancestry local genetic correlation estimation using summary statistics