Question: How to test differential methylated regions in R
0
gravatar for Shaway
15 months ago by
Shaway0
Shaway0 wrote:

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!

dna methylation cpg island R • 313 views
ADD COMMENTlink modified 15 months ago by Kevin Blighe71k • written 15 months ago by Shaway0
1

Dmr (Differentially Methylated Regions) Identification Software

ADD REPLYlink written 15 months ago by ATpoint46k
0
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.

Kevin

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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