This repository contains all the supplementary files and/or R code to generate all the data used in the article: “Refinement of computational identification of somatic copy number alterations using DNA methylation microarrays illustrated in cancers of unknown primary”.
cnv.methyl package has been created in order to collect and share all the functions and code used for the pipline. It is written fully in R and you can install the development version from GitHub with:
# install.packages("devtools")
devtools::install_github("https://github.com/ijcBIT/cnv.methyl.git")You can follow the “Manual.Rmd” document with walk-through examples of all the different steps in the pipline.