Here contains all code used for the AD manuscript and output of EWAS summary statistics. Links to be added later.

• Full_ewas_results.tar.gz : Summary statistics for 2 EWAS analyses (before and after bacon correction). Also contains a file to explain the header.
• QC.R: R code used to pre-process phenotypic and epigenetic data.
• calculateEWAS.R: R code used to calculate EWAS. Note bacon correction calculation is NOT in this file.
• summarizeEwas.R: R code to summarize and make plots using the output from the above code. Note that bacon correction calculation is here.
• fit_allLasso_byChrom.R: R code for the main multivariate analysis.
• checkCLSA.R: R code for replication study using CLSA data. Details see Supplementary Section 1
• examine_34probes_interaction.R: R code to examine interactions. Details see Supplementary Section 3.