perturb_network: Perturbs the connections in a network
In tgrimes/SeqNet: Generate RNA-Seq Data from Gene-Gene Association Networks

Description Usage Arguments Value Examples

The network is perturbed by removing connections from hubs and/or rewiring other nodes in the network. By default, one hub is turned off (i.e. its connections are removed each with probability 'rewire_hub_prob' = 0.5), and no other nodes are changed. Hub nodes are defined as those having degree above three standard deviations from the average degree, and nodes are sampled from these to be turned off; if there are no hub nodes, then those with the largest degree are turned off.

1 2	perturb_network(network, n_hubs = 1, n_nodes = 0, rewire_hub_prob = 0.5, rewire_other_prob = 0.5, ...)

`network`	The network to modify.
`n_hubs`	The number of hub nodes to turn off.
`n_nodes`	The number of non-hub nodes to rewire. When rewiring, the degree of the node is unchanged.
`rewire_hub_prob`	The probability that a connection is removed from a hub that is selected to be turned off. If 'rewire_hub_prob' = 1, then all of the connections to the hub are removed.
`rewire_other_prob`	The probability that a connection is rewired from a non-hub that is selected for rewiring. If 'rewire_other_prob' = 1, then all of the connections to the hub are rewired; however, this does not mean that all connections will be changed, as some connections may be removed but later rewired back.
`...`	Additional arguments passed to rewire_connections_to_node() and remove_connections_to_node()

The modified network.

# Create a random network, perturb the network, then plot the differential network.
set.seed(12345)
nw <- random_network(100)
# Rewire 2 random hub genes and 10 other random genes:
nw_diff <- perturb_network(nw, n_hubs = 2, n_nodes = 10)
plot_network_diff(nw, nw_diff)