title: tmle.npvi: targeted, integrative search of associations between DNA copy number and gene expression, accounting for DNA methylation.
abstract: We describe the implementation of the method introduced by Chambaz et al. in 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.
  
  
  METHODS
  An open-source R package tmle.npvi is available from CRAN (http://cran.r-project.org/).
  
  
  BACKGROUND
  pierre.neuvial@genopole.cnrs.fr.
authors.affiliation: Modal'X, Université Paris Ouest Nanterre, Nanterre, France and Laboratoire de Mathématiques et Modélisation d'Évry, Université d'Évry val d'Essonne, UMR CNRS 8071, ENSIIE, USC INRA, Évry, France.
authors.forename: Antoine
authors.initials: A
authors.lastname: Chambaz
authors.affiliation: Modal'X, Université Paris Ouest Nanterre, Nanterre, France and Laboratoire de Mathématiques et Modélisation d'Évry, Université d'Évry val d'Essonne, UMR CNRS 8071, ENSIIE, USC INRA, Évry, France.
authors.forename: Pierre
authors.initials: P
authors.lastname: Neuvial
mesh_terms: D000465:Algorithms; D001943:Breast Neoplasms / Q000235:genetics*; D019295:Computational Biology / Q000379:methods*; D056915:DNA Copy Number Variations; D019175:DNA Methylation; D005260:Female; D020869:Gene Expression Profiling; D015972:Gene Expression Regulation, Neoplastic; D015894:Genome, Human; D006801:Humans; D012984:Software