Question: How to test differential methylated regions in R
gravatar for Shaway
15 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 • 313 views
ADD COMMENTlink modified 15 months ago by Kevin Blighe71k • written 15 months ago by Shaway0

Dmr (Differentially Methylated Regions) Identification Software

ADD REPLYlink written 15 months ago by ATpoint46k
gravatar for Kevin Blighe
15 months ago by
Kevin Blighe71k
Republic of Ireland
Kevin Blighe71k 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 15 months ago by Kevin Blighe71k

Thank you every much!

ADD REPLYlink written 14 months ago by Shaway0
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