methylKit
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al2na
R package for DNA methylation analysis
Right now we are requiring a numeric vector for treatment groups of samples, but it might make sense to be a bit more flexible and allow more explanatory strings. This...
There are some code conventions used to write a human-readable code. There exist a Google's R Style Guide - https://google.github.io/styleguide/Rguide.xml which is one of the most popular in the R...
This is a feature request against the development version, which contains an `adjust.methylC` feature that does subtraction of an oxBS and mkBS (mock-BS or BS sample). See the code below....
The correlation plot matrix does not have a colour scale for the colour densities. Could a scale be added to help make more sense of the plots.
Hi Alex, during my analysis I came across the issue that the tileMethylCounts() function's argument "dbdir=" does not work in combination with a methylRawListDB object. The output will rather be...
Hi, I am able to run calculateDiffMeth on my dataset when dispersion='none', but get the following error when dispersion='MN': two groups detected: will calculate methylation difference as the difference of...
How to merge when reading multiple files using readMethylDB? myobj
Hi, My methylationstats profile doesn't look like what is in the vignette. Is this a computational issue or does this suggest a specific sample issue? Thanks
There is a `v` before the quote of the version that prevent it from being correctly evaluated: https://github.com/al2na/methylKit/blob/0a5581c33accb8493f00658325fc1d8c4a6370c8/vignettes/methylKit.Rmd#L2 It should be > title: "methylKit: User Guide `r packageVersion('methylKit')`" This is...
