Rtreemix

Rtreemix estimates mutagenetic tree mixture models from cross-sectional genetic data to model the ordered accumulation of permanent changes in evolutionary pathways underlying disease progression and is implemented as an R package.

Key Features:

• Mixture models estimation: Estimates mixture models of mutagenetic trees from observed cross-sectional genetic data to represent alternative evolutionary pathways.
• Genetic progression scores: Derives quantitative genetic progression scores for individual samples based on fitted mutagenetic tree mixtures.
• Model fitting and likelihood computations: Provides functions for fitting mutagenetic tree mixture models and computing likelihoods for parameter estimation.
• Model comparisons and stability analysis: Enables comparison of different evolutionary models and assessment of the stability of estimated mixture components.
• Confidence intervals estimation: Computes confidence intervals for model parameters to quantify estimation uncertainty.
• Waiting time estimations: Estimates waiting times associated with evolutionary events represented in the mutagenetic trees.

Scientific Applications:

• Oncology: Models the accumulation of chromosomal alterations and ordered genetic changes in cancer using cross-sectional data.
• Virology (HIV): Models the ordered accumulation of drug resistance mutations in HIV to study evolutionary pathways of resistance.

Methodology:

Constructs and fits mutagenetic tree mixture models to cross-sectional genetic data, performs likelihood computations for parameter estimation, derives genetic progression scores, estimates confidence intervals and waiting times, and performs model comparisons and stability analyses.