The following scripts are used to run the PGC PTSD EWAS Working Group's longitudinal analysis. The analysis steps are as follows:

Use the script Model1.R to perform a linear mixed model with DNAm values at both time points as the dependent variable, PTSS at both time points as a main effect, and a random intercept for subject, including Age,cell proportions, and ancestry PCs derived from DNAm data were included as covariates.

Use the script Model2.R to conduct a longitudinal analysis using a linear regression model, where post-deployment DNAm was modeled as a function of change in PTSS while adjusting for pre-deployment DNAm, PCs for ancestry, and changes in age (i.e. time passed between pre- and post-deployment data collection), CD8T+, CD4T+, NK, B cell, and monocyte cell proportions.

Use the script MetaAnalysis.R to perform a meta-analysis using weighted sum of z-scores method for Model 1 and Model 2.

Use the script DMRcate_usingSumStats.R to conduct DMR analysis, using summary statisticts from each meta-analysis.