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

_images/beta_pvalue_dist.png

Correlation of p-values of dmc_ttest.py, dmc_glm.py, dmc_nonparametric.py (U test), and dmc_Bayes.py

_images/beta_pvalue_corr.png