HSCT GvHD GWAS and gene expression meta-analysis
This repository contains the scripts for running gene-level p-value summarization from Plink-formatted GWAS results using MAGMA, downloading and processing gene expression data from GEO, and rank-based meta-analysis combining these data.
Published article: Hyvärinen K, Koskela S, Niittyvuopio R, Nihtinen A, Volin L, Salmenniemi U, Putkonen M, Bũno I, Gallardo D, Itälä-Remes M, Partanen J and Ritari J. Meta-analysis of genome-wide association and gene expression studies implicates donor T cell and cytokine pathways in acute GvHD. Front. Immunol. 03 February 2020; https://doi.org/10.3389/fimmu.2020.00019.
main_csc_magma.sh Shell script for calling subscripts for running MAGMA analysis
AGVHD.R R script for running meta-analysis and plotting for aGvHD data