methylKit
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al2na
R package for DNA methylation analysis
It seems as if the caching of uncompressed files introduced with version 1.13.2 causes some problems if the user works with tabix files for more than one CpG context and...
Hi, I was excited to see that newer versions of methylKit allow more than 2 groups. I currently have 4 groups and have used methylkit to call deferentially methylated regions...
Hello, regionCounts() just threw me an error: ``` Error in validObject(.Object) : invalid class “methylBaseDB” object: 1: invalid object for slot "coverage.index" in class "methylBaseDB": got class "NULL", should be...
Hi again Altuna, Finally I solved the problem with my big size files using methylDackel as you recommended (thanks again!). So I have been able to start using methylkit and...
How to merge the DMR within 100bp or other size?
Hi guys, I added parallel methSeg() with methylDB objects and non-tabix objects. I separated code for running fastseg and mclust into two auxiliary function .run.fastseg and .run.mclust. Parallelization is in...
Hello Would it be possible the let the getCorrelation function return the correlation matrix instead of just printing it? Now it is very hard to do anything more with that...
miyakokodama commented 3 minutes ago Hi, I am new to methylKit, I am currently trying to read my bam files with processBismarkAln however I get an error message I don't...
``` #' Find regions of differential methylation #' #' This function performs unsupervised segmentation of #' the methylation differences calculated from calculateDiffMeth. #' Then it classifies hyper and hypo methylated...