Question: How to test differential methylated regions in R
gravatar for Shaway
6 months ago by
Shaway0 wrote:


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!

dna methylation cpg island R • 170 views
ADD COMMENTlink modified 6 months ago by Kevin Blighe60k • written 6 months ago by Shaway0

Dmr (Differentially Methylated Regions) Identification Software

ADD REPLYlink written 6 months ago by ATpoint34k
gravatar for Kevin Blighe
6 months ago by
Kevin Blighe60k
Kevin Blighe60k wrote:

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.


ADD COMMENTlink written 6 months ago by Kevin Blighe60k

Thank you every much!

ADD REPLYlink written 5 months ago by Shaway0
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