methylKit
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al2na
R package for DNA methylation analysis
Right now the error is not handled well.
Hello, I ran calculateDiffMeth with a treatment vector length of 8 and I am unsure how the comparisons are made in this context. Are all comparisons made or are 7...
Dear author, I have two platform generated methylation data. The coverage of Platform1 is very high >25x, however, Platform2's data coverage is very low ~3-5x. Each platform I have one...
Hello, I used nfcore/methylseq pipeline to analyze my data and it worked well. My raw data have been obtained by affinity enrichment , binding the CpG with Human MBD2A (Not...
Hi Dr. Akalin, Thank you for providing such great tool. We just encountered some errors when unite myobj with hundreds of samples. I even ran it with the maximum memory...
I have 4 group and each have 3 replicates, how can i plot the correction of these samples? Thanks
This has something to do with the destranding part of the unite function. For destranding we are processing the methylRawDB in chunks and I assume that somehow the strand-paired cytosines...
Hi, I am using methylkit for my RRBS data. I do have some covariates too which I want to use and check their effect to in our treatments too. I...
When talking about the batch correction (https://github.com/al2na/methylKit/blob/ab60a62e0bd610718fcbb76e9505957c8c3ec15f/vignettes/methylKit.Rmd#L360-L369), we should probably be more explicit about the output of `assocComp()` (https://github.com/al2na/methylKit/blob/ab60a62e0bd610718fcbb76e9505957c8c3ec15f/R/batchControl.R#L180-L185). This recent issue (https://github.com/al2na/methylKit/issues/247 ) shows that people might not be...