R script used in the manuscript entitled " Integrative modeling of tumor DNA methylation identifies a role for metabolism"
This repository contains the R script used to generate results presented in the manuscript by Mahya Mehrmohamadi et al. All data used as input were obtained from the TCGA data portal (https://tcga-data.nci.nih.gov/tcga/tcgaHome2.jsp) and are publically available through the TCGA and therefore not included in this Git repository.
Furthermore, 8 different cancer types were studied in the above mentioned manuscript using the same algorithms. The R script used for one cancer type (brain lower grade glioma or LGG) is provided here as an example. Other cancers were analyzed using the same script with changes to the directory and output/input names and some minor changes in the parameters as needed.
The script used for other cacners can be made available to those who are interested upon request (email mm2489ATcornell.edu)