al2na / methylKit

R package for DNA methylation analysis
https://bioconductor.org/packages/release/bioc/html/methylKit.html
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uniting objects with "base" resolution and strand "*" breaks when requesting destranding #271

Open alexg9010 opened 1 year ago

alexg9010 commented 1 year ago
library(methylKit)
data(methylKit)

mdb <- makeMethylDB(methylRawList.obj)     

# works for "base" -resolution
unite(mdb,destrand=TRUE)
mdb # is fine

# breaks for "region" -resolution
mdbt <- tileMethylCounts(mdb) 
mdbt <- methylRawListDB(lapply(mdbt, function(x) {x@resolution <- "base"; x}),treatment = getTreatment(mdb))
# works
unite(mdbt)    

unite(mdbt,destrand=TRUE)    
> destranding...
> Error in getTabixByChunk(tbxFile, chunk.size = nrow, return.type) : 
>  the tabix file seems to be empty. stopping here.
alexg9010 commented 1 year ago

related to #282