I have 16 RRBS samples: 4 control-female, 4 control-male, 4 treatment female, 4 treatment-male.
I wanna analyse for DMR using methylkit.
I can easily divide them to two analysis (8 samples each) and perform one for female control vs treatment ,and male control vs treatment.
I however, want to also be able to normalize the methylation data among all samples and selected the bases that has been covered in all positions in all 16 samples, and then find the DMR for each female and male. Is that possible?
Following code will result in meth object to be used in MDR analysis. Is there a way to separate samples after I have meth? so that I can find the DMR for each male and female?
obj=methRead(location=file.list,sample.id, assembly="hg38", treatment= treatment, context="CpG")meth=unite(filtered.obj, min.per.group=1L, destrand=FALSE) filtered.obj=filterByCoverage(obj,lo.count=10,lo.perc=NULL, hi.count=NULL,hi.perc=99.9) normalizeCoverage(filtered.obj,method="median") meth=unite(filtered.obj)