GXwasR Tutorials

Welcome to the GXwasR tutorial hub — a central location for learning how to use the GXwasR R package for genome-wide and x-chromosome wide association studies, quality control, ancestry estimation, and more.

⚠️ These tutorials are now available via the GXwasR pkgdown site, though this repository remains as a familiar entry point for users and contributors.

📘 Available Tutorials

🔍 Overview

• Getting to Know GXwasR

  An introduction to the core functionality and structure of the package.

🧹 Quality Control

• Pre-Imputation QC

  Data filtering and preparation before imputation.

• Post-Imputation QC

  Evaluating and refining data quality after imputation.

🧬 Association Testing

• GWAS, XWAS, and Sex-Differential Models

  Running association models using GXwasR.

🧠 Polygenic Score

• Polygenic Score (PGS)

  Calculating and interpreting PGS using summary stats and genotype data.

🌍 Ancestry & Population Structure

• Ancestry Estimation

  Estimate population structure using reference panels and PCA/SVD.

• Heritability Estimation

🔗 Meta Analysis & Correlation

• Meta Analysis

  Combine association results across datasets.

• Genetic Correlation from Summary Statistics

  Estimate genetic correlation using summary-level data.