intcomp: a benchmarking pipeline for integrative
cancer gene detection
Leo Lahti*¹, Martin Schäfer², Hans-Ulrich Klein³, Silvio
Bicciato4; and Martin Dugas³
(1) Wageningen University, Netherlands. (2) TU Dortmund University, Germany (3) University of Münster,
Germany (4) University of Modena and Reggio Emilia, Italy.
The intcomp R
package provides a benchmarking tools for quantitative comparison
of cancer gene detection algorithms based on integrative analysis of
DNA copy number and gene expression data.
The cancer gene prioritization performance of the methods is compared
with respect to golden-standard lists of known cancer genes in real
and simulated data sets .
The comparison methods include variants of
SIM and Ortiz-Estevez.
The current version focuses on cancer gene prioritization
performance of these algorithms. Contributions for further methods,
data sets and benchmarking procedures are welcome.
Download the source code package
sources are also available through SVN from R-Forge. See
for installation instructions, package dependencies, further details
The benchmarking results reported in Briefings in Bioinformatics 
are available as R data files from the results
This work was supported by EuGESMA COST Action BM0801 (European
Genomics and Epigenomics Study on MDS and AML). The work is licensed
under the FreeBSD open
source license. Your feedback and contributions are welcome.
See the project page at
R-Forge, or contact project
- Lahti L, Schäfer M, Klein H-U, Bicciato S, and Dugas
M. Cancer gene prioritization by integrative analysis of mRNA
expression and DNA copy number data: a comparative review. Briefings
in Bioinformatics. Online March 2012. (Abstract;