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!
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written
by
carlos_marchi
1 answer
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).
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