# 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

1 | ```
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

1 2 3 4 5 | ```
## NOT RUN
## The computation of the maximum likelihood tree model needs longer run time.
#data(kidney)
#y <- MLtopology(kidney$x)
## END(NOT RUN)
``` |

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