This repository is the analysis code used for the manuscript, "Genome-wide sequencing-based identification of methylation quantitative trait loci and their role in schizophrenia risk" by Perzel Mandell et al.: https://www.nature.com/articles/s41467-021-25517-3
Herein, we provide the code used for identification of meQTLs and gDMRs, as well as mediation analysis between meQTLs and eQTLs.
Methylation data is stored in bsseq objects, and SNP data is stored as matrixes of allele counts (0,1,2) for each sample, along with a map indicating SNP position and counted allele.