create_modules_for_network: Randomly sample subsets of genes for each module

In 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 indices for genes contained in each module.

References

\insertRef

grimes21SeqNet

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)

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