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

Question

[carlos_marchi]

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!

[Hamid Ghaedi]

You may want to check these posts:

1- Methylation Analysis Tutorial in R_part1

2-Methylation Analysis Tutorial in R_part2

Answer 1

[Marc]

methylize (a python package that is part of the methylsuite) offers a differentially methylated positions (DMP) analysis:

https://life-epigenetics-methylize.readthedocs-hosted.com/en/latest/docs/demo_diff_meth_pos.html

And subsequently, you can do EWAS on differentially methylated regions for your case vs control groups.

Both functions provide p-value analysis with several ways to control for multiple comparisons (bonferoni or FDR).