Description Details Author(s) References Examples
Computing probabilistic tree models for oncogenesis based on genetic data using maximum likelihood.
Package: | oncomodel |
Type: | Package |
Version: | 1.0 |
Date: | 2008-01-18 |
License: | GPL version 2 or newer |
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
von Heydebreck A, Gunawan B, Fuezesi L. 2004. Maximum likelihood estimation of oncogenetic tree models. Biostatistics 5:545-556.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 | ## 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)
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