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How to test differential methylated regions in R

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!

r dna methylation cpg island
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updated by Kevin Blighe Kevin Blighe • written by Shaway • Shaway

1 answer

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

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written by Kevin Blighe Kevin Blighe

Thank you every much!

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written by Shaway • Shaway

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