How to test differential methylated regions in R

Question

[Shaway]

Hello,

I'm doing some research in WGBS and want to distinguish differential methylated CpG island from tumor and normal (10 samples for each group). I tried DMRfinder, but it combine CpGs to form regions, seems do not support customized regions.

I can just compute methylation level for every CpG island(download from UCSC) and do t-test, but I want try several tools to comfirm the results.

Is there any tools/packages to infer differential methylated island from overall CpG islands?

Thanks for your help!

[ATpoint]

Dmr (Differentially Methylated Regions) Identification Software

Answer 1

[Kevin Blighe]

Use the Wilcoxon Rank Sum [paired] test to derive a p-value, and additionally obtain the difference in group (tumour|normal) mean or median as an extra control / filter.

Kevin

[Shaway]

Thank you every much!