Rtreemix -- an R package for estimating evolutionary pathways and genetic progression scores
What you can do:
Estimate the mutagenetic trees mixture models from cross-sectional data and use them for various predictions.
Highlights:
- 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.
Keywords:
- mutagenetic tree
- mixture model
- cancer
- HIV
- disease progression
- genetic progression score
Literature & Tutorials:
This record last updated: 09-03-2008