create_network_from_modules: Create a network object.

In tgrimes/SeqNet: Generate RNA-Seq Data from Gene-Gene Association Networks

Description

Creates a graph with certain features. This network is then used with other sample generating methods to obtain count data. Note: the module structure is used to incorporate general pathways in the graph. These are randomly constructed by generating a small-world graph using the Watts-Strogatz method (implemented through igraph::watts.strogatz.game).

Usage

create_network_from_modules(p, module_list,
  node_names = as.character(1:p), ...)

Arguments

p	The number of nodes in the graph
module_list	A named list of 'network_module' objects.
node_names	(optional) Vector of strings providing names for each node in the graph. Default names are "1", "2", ..., "p".
...	Additional arguments passed to random_module(); only used if modules need to be generated.

Value

A network object.

Examples

# Networks can be crafted manually by first constructing the individual
# modules, then putting them together to create a network.
module_1 <- random_module(1:10) # A module containing nodes 1-10
module_2 <- random_module(5:15) # A module containing nodes 5-15
# Create a network containing 20 nodes and the two modules. 
nw <- create_network_from_modules(20, list(module_1, module_2))
nw 
# Note: nodes 16-20 are not in a module, so they have no connections.
plot(nw)

tgrimes/SeqNet documentation built on Sept. 1, 2020, 7:50 a.m.