Unsupervised method for detecting differentially methylated regions (DMR)

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6.8 years ago

ResearchR ▴ 120

Dear all,

I am working on whole-genome-bisulfite data and would like to detect differentillay methylated regions. When having predefine conditions for each sample (i.e. clinical infromation), this is not a big deal. Since I am working on a more or less mining-project, I would like to know if there is information hidden in my data, which has not been annotated so far. Does anyone of you know an unsupervised-like method for detecting DMRs?

Best Chris

Bisulfite sequencing • 1.5k views

ADD COMMENT • link 6.8 years ago by ResearchR ▴ 120

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Have you tried binning and summarizing (mean, median, for example) your data by genomic coordinate and then making heatmaps?

ADD REPLY • link 6.8 years ago by Sean Davis 27k

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Do you know these papers :

BSmooth, Bisulfighter

ADD REPLY • link 6.8 years ago by arta ▴ 670

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As far as I know, BSmooth and Bisulfighter detect DMRs based in predefined subgroups.

ADD REPLY • link 6.8 years ago by ResearchR ▴ 120

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