# MLtopology {oncomodel}

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.

### 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)