methylKit
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Size of filtered object larger than before filtering
#H1 <- readRDS("data/H1.chr21.chr22.rds")
library("methylKit")
# Load data
fl <- list.files("~/Downloads/", pattern="chr1and2", full.names = T)
rawmeth=methRead(as.list(fl), sample.id = list("nbm1","nbm2","idh1","idh2"),treatment=c(0,0,1,1), context="CpG", assembly="hg18")
filtered.meth=filterByCoverage(rawmeth,lo.count=10,lo.perc=NULL, hi.count=NULL,hi.perc=99.9)