simOGraph: Simulate oncogenetic/CBN/XMPN DAGs.

In OncoSimulR: Forward Genetic Simulation of Cancer Progression with Epistasis

Description

Simulate DAGs that represent restrictions in the accumulation of mutations.

Usage

simOGraph(n, h = ifelse(n >= 4, 4, n), conjunction = TRUE, nparents = 3,
multilevelParent = TRUE, removeDirectIndirect = TRUE, rootName = "Root",
geneNames = seq.int(n), out = c("adjmat", "rT"),
s = 0.1, sh = -0.1, typeDep = "AND")

Arguments

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 conjunction is TRUE.
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 non-root nodes.
out	Whether the ouptut should be an adjacency matrix or a "restriction table", as used in allFitnessEffects.
s	If using as output a restriction, the default value for s. See allFitnessEffects.
sh	If using as output a restriction, the default value for sh. See allFitnessEffects
typeDep	If using as output a restriction, the default value for "typeDep". See allFitnessEffects

Details

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.

Value

An adjacency matrix for a directed graph or a data frame to be used as input, as "restriction table" in allFitnessEffects.

Author(s)

Ramon Diaz-Uriarte. 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

Examples

(a1 <- simOGraph(10))
library(graph) ## for simple plotting
plot(as(a1, "graphNEL"))

simOGraph(3, geneNames = LETTERS[1:3])

OncoSimulR documentation built on Nov. 8, 2020, 8:31 p.m.