Reference: Schultz et al. (2015) Nature. doi:10.1038/nature14464 See pages 4-8 of Supp. Material

  • Methylkit:
    1. calculateDiffMeth uses a logistic regression model to test if treatment has any effect on CpG (loci) methylation or region methylation.
      • is log(πi/(1−πi))=β0+β1Treatmenti a “better” model than log(πi/(1−πi))=β0 ?
      • a q-value is calculated and a cutoff can be defined to select significant DMLs or DMRs
        • this method is only capable of comparing two groups at a time.

Reference: methylkit documentation, see section 3.6

  • DMGs:
    1. bionmial glm comparison between methylated and non-methylated CpGs
      • glm (methylated,non_methylated ~ pH * position, family = “binomial”)
      • each treatment replicate is compared to a control replicate in a combinatorial fashion to assign equal weightage to each replicate
    2. Liew also does glm on mean % methylation with gaussian method

Reference Liew et al. (2018) Science Advances