Summary: We describe the implementation of the method introduced by Chambaz et al. (2012). We also demonstrate its genome-wide application to the integrative search of new regions with strong association between DNA copy number and gene expression accounting for DNA methylation in breast cancers.

Availability and implementation: An open-source R package tmle.npvi is available from CRAN (http://cran.r-project.org/).

Contact: pierre.neuvial@genopole.cnrs.fr