CNAmet R package

CNAmet is an algorithm and R package to prioritize putative cancer driver genes by integrating copy number, DNA methylation and expression data. Outputs of our algorithm include scores for methylation alteration induced expression, copy number aberration induced expression, a score for their combined effect, and adjacent p-values, which are also multiple hypothesis corrected.

In addition to the CNAmet algorithm, our R package includes the S2N algorithm for the integration of copy number to expression data. The CNAmet algorithm is also implemented as a component in the Anduril bioinformatics framework.



There are three versions of the R package.

Installation and algorithm details are discussed in the user guide and how-to article.

The glioblastoma multiforme (GBM) data, which are used for the case study in the CNAmet article, are also available for download.

  • GBM sample data 1 (gene expression, and hypomethylation and copy-number gain calls)
  • GBM sample data 2 (gene expression, and hypermethylation and copy-number deletion calls)


Louhimo, R. and Hautaniemi, S. CNAmet: an R package for integration of copy number, expression and methylation data Bioinformatics (2011) 27(6):887-888.


The source code of the case study written in Anduril script can be found here.

The article contains two case study - one with glioblastoma multiforme (GBM) and the other with ovarian cancer (OV) data. Both belong to larger analyses. The complete GBM data analysis can found as a part of the Anduril framework casestudy which is frequently updated. The ovarian cancer analysis results can be found here.

We invite you to browse and use these results freely, and we request you to cite either the Anduril (for GBM) or CNAmet article (for OV) in such cases.

Related websites

Web site copyright Systems Biology Laboratory, University of Helsinki.
CNAmet copyright © 2010-2013 Riku Louhimo.
Page last updated 1 July 2013