Maximum likelihood tree models for oncogenesis

Description

Computing probabilistic tree models for oncogenesis based on genetic data using maximum likelihood.

Details

Package: oncomodel
Type: Package
Version: 1.0
Date: 2008-01-18
License: GPL version 2 or newer

Author(s)

original by Anja von Heydebreck anja.von.heydebreck@merck.de, contributions from Christiane Heiss christiane.heiss@web.de Maintainer: Anja von Heydebreck anja.von.heydebreck@merck.de

References

von Heydebreck A, Gunawan B, Fuezesi L. 2004. Maximum likelihood estimation of oncogenetic tree models. Biostatistics 5:545-556.

Examples

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  ## NOT RUN
  ## The example needs longer run time.
  #data(kidney)
  ##  Maximum likelihood tree model
  #y <- MLtopology(kidney$x)
  
  ## Graphical presentation
  #y.phyl <- newick2phylog(y$newick)
  #plot.phylog(y.phyl, cnodes =1,  clabel.n=0.6, f=0.75, sub="Oncogenetic tree of given aberrations")

  ## Bootstrap confidence values (in percent) and the splits occurring in
  ## more than 10 percent of the bootstrap data sets 
  #boot.conf.values(kidney$x, nrep=2)

  ## Probability for aberration -3|-3p
  #leafset.prob(c("-3|-3p", "+5|+5q"), kidney$res)

  ## Probability for aberration -3|-3p
  #leafset.prob2(c("-3|-3p", "+5|+5q"), kidney$res)
  ## END(NOT RUN)