Scripts accompanying the manuscript 'Genome-wide study of DNA methylation in ALS implicates metabolic, inflammatory and cholesterol pathways'.

EWAS_main.Rmd: All EWAS analyses (including sensitivity analyses), invokes several scripts in the utils/ folder. Analyses are submitted on a slurm hpc.
EWAS_finetuningPCs.Rmd: Fine-tuning the number of PCs for the LB algorithm.
EWAS_sensitivity.Rmd: Plots sensitivity analyses + run leave-one-out analyses.
EWAS_plots.Rmd: Main figure 1 of the manuscript.
EWASdb_enrichments.Rmd: EWASdb enrichments + plots (including main figure 2).
getPMS.R: Generate PMSs using published coefficients.
incremental_R2.Rmd: PMS validation.
PMS_main.Rmd: PMS case/con and survival analyses + plots (including main figure 3).
Survival_analyses.Rmd: Survival analyses of DMPs.

utils/: several wrapper scripts invoked in EWAS_main.Rmd.