The analyses at the longer spatial scales – DMRs and blocks – both utilized the above linear model; DMR analysis generally finds contiguous CpGs where βi ≠ 0 whereas block analysis first collapses the methylation proportions into one level across neighboring probes per sample (e.g. pijk¯→rij), fits the above model. Regional analysis to find differentially methylated regions (DMRs) and “block finding” were performed using the minfi R package49 using the bumphunterEngine and blockFinder functions, respectively, each with 1000 linear model bootstrap iterations18 and a cutoff of 0.1 (corresponding to contiguous probes with a minimum 10% directionally consistent change in DNAm associated with birth, e.g. |β̂i| > 0.1), with other parameters in these minfi functions set to their default values.
