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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.
