MLtopology {oncomodel}

Compute Maximum Likelihood Tree Topology

Package:

oncomodel

Version:

1.0

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.

Values

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)

Documentation reproduced from package oncomodel, version 1.0. License: GPL (>= 2)