Alexander Blume

Hi @priyatamapandey, Sorry for the late reply, I'll try to help you with your questions. Concerning the batch correction, the `association` values that are part of the `assocComp()` output shows...

Hi @yplee614, there is no function to merge dmcs to dmrs within a certain range, but you could look at the function described here: https://github.com/al2na/methylKit/issues/193 , which clusters dmcs into...

Ah Okay, there is also no function to merge dmrs within a certain range, but I guess one could do this with findOverlaps() and some checks to only merge dmrs...

Hi @iramai Could you please send us the output of your session info, so we know which version of methylKit you are using. Best, Alex

Hi @yplee614, are you referring to the function `getCorrelation()` and want to calculate the correlation of samples? The function `getCorrelation` does not use the information of the treatment value, thus...

@katwre it would be cool if you do this. Thanks!

Hi @boryanakis, it seems like you are having duplicated chromosome positions in your methylBase object. Could you please tell me which version of methylKit you are using and show me...

Dependencies can be easily tracked with https://cran.r-project.org/web/packages/miniCRAN/vignettes/miniCRAN-dependency-graph.html .

we could probably also have rtracklayer as an optional dependency.

Hi @erikras12, You are basically running a logistic regression with eight groups. The methylation difference at each given site will correspond to the maximal methylation difference between the groups: https://github.com/al2na/methylKit/blob/9620cd686a14483f2158c75805c952d066c7b7f8/R/diffMeth.R#L306-L312...