Those equally methylated regions can be found in the regions that were not significant differentially methylated regions.

applying a p value or FDR threshold filter and methylation differences (like

Once you found the DMRs with your significance thresholds (P.Adj and FC), then you can state that all the other analyzed regions are not differentially methylated because they fall above the thresholds. The most used R package for this kind of analysis is limma.

Hi Tushar, 

If I kept well your question I agree with Ferdinando and Wei you can consider the !DMR, the not significant regions.

I suggest you to try the function TCGAanalyze_DMR and TCGAVisualize_volcano from our new package TCGAbiolinks.

In particular you can take a look in our NAR paper or related Bionconductor's vignette.

https://www.bioconductor.org/packages/release/bioc/vignettes/TCGAbiolinks/inst/doc/tcgaBiolinks.html

For further informations or collaborations you can write me ([email protected]).

Article TCGAbiolinks: An R/Bioconductor package for integrative anal...