connect_module_structure: Connect disconnected components in an adjacency matrix

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

Description

Connect disconnected components in an adjacency matrix

Usage

connect_module_structure(
  adj,
  weights = NULL,
  alpha = 100,
  beta = 1,
  epsilon = 10^-5
)

Arguments

adj	An adjacency matrix to modify.
weights	(Optional) weights used for sampling nodes.
alpha	A positive value used to parameterize the Beta distribution.
beta	A positive value used to parameterize the Beta distribution.
epsilon	A small constant added to the sampling probability of each node.

Value

A modified adjacency matrix

Note

This function is used in random_module_structure to reconnect any disconnected components after edge removal and rewiring. When connecting two components, a node is sampled from each component with probability that is dependent on node degree; those two nodes are then connected, which connects the components.

Examples

# This function is used in `random_module_structure()` to reconnect any
# disconnected components. To demonstrate, we'll create a random structure,
# remove connections to one of the nodes (that node will then be a disconnected
# component), and use `connect_module_structure()` to reconnect it back to
# the main component.
adj <- random_module_structure(10)
adj <- remove_connections_to_node(adj, 1, prob_remove = 1)
# Note that there are now two components in the network:
components_in_adjacency(adj) 
g <- plot_network(adj)
# After connecting, the network contains one component.
adj <- connect_module_structure(adj)
components_in_adjacency(adj) 
plot_network(adj, g)

SeqNet documentation built on July 9, 2021, 9:08 a.m.