Alexander Blume
Alexander Blume
Right now the error is not handled well.
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...
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...
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...
``` #' Find regions of differential methylation #' #' This function performs unsupervised segmentation of #' the methylation differences calculated from calculateDiffMeth. #' Then it classifies hyper and hypo methylated...
Based on the new badge showing all package deps https://bioconductor.org/packages/release/bioc/html/methylKit.html#since introduced on Bioc we are having 87 deps in total.  I was dazzled to see that we have ggplot2...
https://github.com/al2na/methylKit/blob/a22fb817a1c244ccba0491b9289064731c801a30/R/bedgraph.R#L78
See here, the error is not very informative https://groups.google.com/d/msg/methylkit_discussion/9nPkCbPyKLI/a9xCm3mdAwAJ
example: ``` library(methylKit) file.list=system.file("extdata", "test1.myCpG.txt", package = "methylKit") myobj=methRead( file.list, sample.id="test1", assembly="hg18",treatment=c(1,1,0,0), dbtype="tabix") readTabixHeader(getDBPath(myobj)[[1]]) > $dbtype [1] "tabix" $sample.ids [1] "test1" $assembly [1] "hg18" $context [1] "CpG" $resolution [1] "base"...