create_modules_for_network: Randomly sample subsets of genes for each module

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

Description

Creates a collection of modules containing randomly samples genes.

Usage

create_modules_for_network(n_modules, p, avg_module_size = 50,
  sd_module_size = 50, min_module_size = 10, max_module_size = 200,
  sample_link_nodes_fn = sample_link_nodes,
  sample_module_nodes_fn = sample_module_nodes, ...)

Arguments

n_modules	The number of modules to include in the network.
p	The number of nodes in the network.
avg_module_size	The average number of nodes in a module.
sd_module_size	The standard deviation of module size.
min_module_size	The minimum number of nodes in a module.
max_module_size	A positive value. Any generated module sizes above this value will be reduced to 'max_module_size'. Set to 'Inf' to avoid this truncation.
sample_link_nodes_fn	A function used for sampling link nodes for a new module.
sample_module_nodes_fn	A function used for sampling nodes for a new module.
...	Additional arguments passed to random_module().

Value

A list containing the indicies for genes contained in each module.

Examples

# Create a two modules (having random structures and sizes) from a pool 
# of 100 nodes.
create_modules_for_network(n_modules = 2, p = 100)
# Set n_modules = NULL to continue making modules until all nodes have
# been selected at least once.
create_modules_for_network(n_modules = NULL, p = 100)

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