1. Compare Differential CpG Analysis Tools¶
| Program | Input data | Method/Model | Co-variable |
| dmc_fisher.py | Proportion value (RRBS/WGBS) | Fisher’s exact test | No |
| dmc_logit.py | Proportion value (RRBS/WGBS) | Logistic regression (binom or quasi-binom) | Yes |
| dmc_bb.py | Proportion value (RRBS/WGBS) | Beta-binomial regression | Yes |
| dmc_ttest.py | Beta- or M-value (450K/850K) | Student’s T-test or ANOVA | No |
| dmc_glm.py | Beta- or M-value (450K/850K) | Generalized linear model | Yes |
| dmc_nonparametric.py | Beta- or M-value (450K/850K) | Mann–Whitney U test or Kruskal-Wallis H test | No |
| dmc_Bayes.py | Beta- or M-value (450K/850K) | Bayes estimation | No |
2. P-value distributions¶
Compare p-value distributions of dmc_ttest.py, dmc_glm.py, dmc_nonparametric.py (U test), and dmc_Bayes.py
Correlation of p-values of dmc_ttest.py, dmc_glm.py, dmc_nonparametric.py (U test), and dmc_Bayes.py
