Tries to compute the maximum likelihood tree model for a given data set through stepwise leaf insertion and rearrangements.
MLtopology(x, verbose = FALSE)
- a binary matrix with rows representing tumors and columns representing genetic alterations.
- a Boolean value indicating whether intermediate results of the algorithm are to be printed.
A list with the following components:
- the resulting tree in matrix format.
- a vector of the maximum likelihood edge parameters (model probabilities).
- the log-likelihood of the tree model.
- the character vector with the names of alterations.
- the tree model in Newick format.
von Heydebreck A, Gunawan B, Fuezesi L. 2004. Maximum likelihood estimation of oncogenetic tree models. Biostatistics 5:545-556.
## 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)