Question: Unsupervised method for detecting differentially methylated regions (DMR)
gravatar for ResearchR
19 months ago by
ResearchR70 wrote:

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

sequencing bisulfite • 535 views
ADD COMMENTlink written 19 months ago by ResearchR70

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

ADD REPLYlink written 19 months ago by Sean Davis25k

Do you know these papers :

BSmooth, Bisulfighter

ADD REPLYlink modified 19 months ago • written 19 months ago by arta540

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

ADD REPLYlink written 19 months ago by ResearchR70
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