perturb_network {SeqNet}

Perturbs the connections in a network

Description

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.

Usage

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

Arguments

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.

Value

The modified network.

Examples

# 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)