R or python packages for differential methylation levels analysis: case x control

Hi,

There are several txt files in which each corresponds to a patient containing measure methylation levels in both conditionals: case and control. Filename corresponds to patient identification and inside the file contains three columns: gene symbol, case and control. The DNA methylation levels can be B-values or M-values. The HumanMethylation450 used to quantify methylation levels.

So, Is there a R or Python package can read these data and applies the differential methylation levels analysis? Does package show information invoving logFC, P-value, gene is hypermethylated, hypomethylated or none?

Thank you very much!