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Bioinformatics Advance Access originally published online on August 20, 2008
Bioinformatics 2008 24(20):2391-2392; doi:10.1093/bioinformatics/btn410
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© 2008 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

Rtreemix: an R package for estimating evolutionary pathways and genetic progression scores

Jasmina Bogojeska 1,*, Adrian Alexa 1, André Altmann 1, Thomas Lengauer 1 and Jörg Rahnenführer 2

1Max Planck Institute for Informatics, Campus E1.4, 66123 Saarbrücken and 2Fakultät Statistik Technische Universität Dortmund, Vogelpothsweg 87, 44227 Dortmund, Germany

*To whom correspondence should be addressed.


  Abstract

Summary: In genetics, many evolutionary pathways can be modeled by the ordered accumulation of permanent changes. Mixture models of mutagenetic trees have been used to describe disease progression in cancer and in HIV. In cancer, progression is modeled by the accumulation of chromosomal gains and losses in tumor cells; in HIV, the accumulation of drug resistance-associated mutations in the viral genome is known to be associated with disease progression. From such evolutionary models, genetic progression scores can be derived that assign measures for the disease state to single patients. Rtreemix is an R package for estimating mixture models of evolutionary pathways from observed cross-sectional data and for estimating associated genetic progression scores. The package also provides extended functionality for estimating confidence intervals for estimated model parameters and for evaluating the stability of the estimated evolutionary mixture models.

Availability: Rtreemix is an R package that is freely available from the Bioconductor project at http://www.bioconductor.org and runs on Linux and Windows.

Contact: jasmina{at}mpi-inf.mpg.de

Associate Editor: Alfonso Valencia

Received on April 19, 2008; revised on June 26, 2008; accepted on July 30, 2008

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