in the fetal samples. For CpG-level analyses, we fit the above linear model with the limma R/Bioconductor package46 to obtain mean differences, moderated t-statistics and corresponding p-values, which we adjusted by the number of tests (i.e. Bonferroni correction47) to conservatively control for multiple testing (as neighboring CpGs tend to be correlated48, reducing the number of effective tests). While some previous manuscripts remove all probes containing SNPs in any position, we observe that the single CpGs that are significantly associated with birth are in fact depleted of probes containing SNPs (OR = 0.79, p < 10–100), as 17.0% of significant CpGs contain an annotated probe SNP compared to 20.6% of non-significant probes.
