CARMA-X is a fine-mapping method designed for admixed populations, leveraging ancestry-specific genotype data derived from local ancestry inference (LAI) tools or summary statistics generated by admixed GWAS methods, like Tractor. It features an innovative approach to estimate cross-ancestry linkage disequilibrium (LD) matrices, enabling robust modeling of ancestry-specific and shared genetic effects. CARMA-X effectively handles diverse genetic architectures and admixture scenarios, addressing challenges posed by LD variations across ancestries.
The CARMA-X webpage https://zikuny.github.io/CARMAX/ provides a detailed walkthrough for setting up and running CARMA-X, including step-by-step instructions and explanations. It guides users through fine-mapping analysis using an example dataset designed to simulate admixed populations, showcasing key features and outputs of the method.
To run the example, first download the example data from the repository to your local directory:
git clone https://github.com/ZikunY/CARMAX.gitOnce the repository is cloned, navigate to the Example directory and run the demonstration script:
CARMAX/Example/Demonstration.R