oncomodel (version 1.0)

MLtopology: Compute Maximum Likelihood Tree Topology

Description

Tries to compute the maximum likelihood tree model for a given data set through stepwise leaf insertion and rearrangements.

Usage

MLtopology(x, verbose = FALSE)

Arguments

x

a binary matrix with rows representing tumors and columns representing genetic alterations.

verbose

a Boolean value indicating whether intermediate results of the algorithm are to be printed.

Value

A list with the following components:

tree

the resulting tree in matrix format.

p

a vector of the maximum likelihood edge parameters (model probabilities).

totloglik

the log-likelihood of the tree model.

var.names

the character vector with the names of alterations.

newick

the tree model in Newick format.

References

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

Examples

  ## NOT RUN
  ## The computation of the maximum likelihood tree model needs longer run time.
  #data(kidney)
  #y <- MLtopology(kidney$x)
  ## END(NOT RUN)