methylKit
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al2na
R package for DNA methylation analysis
Hi, When methylation difference is calculated there are 3 options for effect size calculation: weighted mean, unweighted mean and model prediction (`predicted`). All of these options calculate or estimate effect...
Hello, I've been using MethylKit to analyse RRBS data from human samples and I noticed that when I introduce covariates with one or more NAs in them (e.g. if one...
I have a dataframe that was extracted from a methylBase object using `getData()` - it retains the same columns as a methylBase object - I'd now like to convert it...
I have thoroughly enjoyed using methylkit’s beta value simulation and I am having trouble seeing how this is similar to real data. I am attaching a correlation plot between beta...
Hi, I'm experiencing the following issue when running the calculateDiffMeth function: `calculateDiffMeth(data_obj, mc.cores = 32 , overdispersion = "MN" , test = "Chisq")` and I get the error: `two groups...
Hi, I am analysing data from two batches and I would like to check if there are batch effects. The assocComp function returns association p-values (eg: $batch_id PC1 PC2 PC3...
Hi! I have followed the protocol of methylkit, but when I arrive to the annotation step, I have an error, related to themethylobject conversion to GRanges. I write here, few...
Hi! I have been trying to use methylkit for Bisulfite Sequencing samples. Finally I have achieved the differentially methylated regions list with the %methylation value and I would like to...
https://github.com/al2na/methylKit/issues/224 When methylation difference is calculated there are 3 options for effect size calculation: weighted mean, unweighted mean and model prediction (`predicted`). All of these options calculate or estimate effect...