Description Usage Arguments Value References Examples
Tries to compute the maximum likelihood tree model for a given data set through stepwise leaf insertion and rearrangements.
1 | MLtopology(x, verbose = FALSE)
|
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. |
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. |
von Heydebreck A, Gunawan B, Fuezesi L. 2004. Maximum likelihood estimation of oncogenetic tree models. Biostatistics 5:545-556.
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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