Hi, I have completed my first DMR analysis with the 450k array data using RnBeads. The final differential analysis line of code was:
But an enrichment analysis wasn't run. Here are my options.
rnb.options(filtering.sex.chromosomes.removal=TRUE, identifiers.column= "Sample_ID", import.table.separator="\t", "differential.comparison.columns"=c("TumorNormal"), "columns.pairing"=c("TumorNormal"="Sample_Name"), inference.targets.sva=c("Sample_Group"), inference.sva.num.method="be")
I assume that I forgot to put something here, but any help would be appreciated. I'd like to run my enrichment analysis on my differentially methylated regions (genes).