Description Usage Arguments Details Value Author(s) Examples
View source: R/generaterandomtrees.R
Simulate DAGs that represent restrictions in the accumulation of mutations.
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n 
Number of nodes, or edges, in the graph. Like the number of genes. 
h 
Approximate height of the graph. See details. 
conjunction 
If TRUE, conjunctions (i.e., multiple parents for a node) are allowed. 
nparents 
Maximum number of parents of a node, when 
multilevelParent 
Can a node have parents at different heights (i.e., parents that are at different distance from the root node)? 
removeDirectIndirect 
Ensure that no two nodes are connected both directly (i.e., with an edge between them) and indirectly, through intermediate nodes. If TRUE, we return the transitive reduction of the DAG. 
rootName 
The name you want to give the "Root" node. 
geneNames 
The names you want to give the the nonroot nodes. 
out 
Whether the ouptut should be an adjacency matrix or a
"restriction table", as used in 
s 
If using as output a restriction, the default value for s. See

sh 
If using as output a restriction, the default value for
sh. See 
typeDep 
If using as output a restriction, the default value for
"typeDep". See 
This is a simple, heuristic procedure for generating graphs of restrictions that seem compatible with published trees in the oncogenetic literature.
The basic procedure is as follows: nodes (argument n
) are split
into approximately equally sized h
groups, and then each node
from a level is connected to nodes chosen randomly from nodes of the
remaing superior (i.e., closer to the Root) levels. The number of
edges comes from a uniform distribution between 1 and nparents
.
The actual depth of the graph can be smaller than h
because
nodes from a level might be connected to superior levels skipping
intermediate ones.
See the vignette for further discussion about arguments.
An adjacency matrix for a directed graph or a data frame to be used as
input, as "restriction table" in allFitnessEffects
.
Ramon DiazUriarte. Code for transitive closure taken from the nem package, whose authors are Holger Froehlich, Florian Markowetz, Achim Tresch, Theresa Niederberger, Christian Bender, Matthias Maneck, Claudio Lottaz, Tim Beissbarth
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