# Generate RNA-Seq Data from Gene-Gene Association Networks

## Documentation for package ‘SeqNet’ version 1.1.0

- DESCRIPTION file.

## Help Pages

A C D E G H I P Q R S U

## -- A --

add_modules_to_network | Internal function for adding a set of modules to the network
add_random_module_to_network | Adds a random module of a given size to the network
all_networks_contain_same_modules | Internal function to check if a list of networks all contain the same modules.
all_networks_contain_same_nodes | Internal function to check if a list of networks all contain the same nodes.
as_single_module | Collapses all modules in network into a single module

## -- C --

check_adjacency_cpp | C++ implementation to check if a matrix is an adjacency matrix
components_in_adjacency | C++ implementation to obtain connected components in a graph.
connect_module_structure | Connect disconnected components in an adjacency matrix
create_cytoscape_file | Create an edge table file for Cytoscape
create_empty_module | Create a module
create_empty_network | Create a network object.
create_modules_for_network | Randomly sample subsets of genes for each module
create_module_from_adjacency_matrix | Create a module from an adjacency matrix
create_module_from_association_matrix | Create a module from an association matrix
create_network_from_adjacency_matrix | Create a network object from an adjacency matrix
create_network_from_association_matrix | Create a network object from an association matrix
create_network_from_modules | Create a network object.

## -- D --

dzinb | The Zero-Inflated Negative Binomial Distribution

## -- E --

ecdf_cpp | C++ implementation of empirical CDF
edges_from_adjacency_cpp | C++ implementation for obtaining an edge list from adjacency matrix
est_params_from_reference | Estimate ZINB parameters from reference data

## -- G --

gen_gaussian | Generate observations from a Gaussian graphical model.
gen_partial_correlations | Generate partial correlations for a list of networks.
gen_rnaseq | Generate RNA-seq data from an underlying network
gen_zinb | Generate ZINB counts from an underlying network
get_adjacency_matrix | Get adjacency matrix
get_adjacency_matrix.default | Get adjacency matrix
get_adjacency_matrix.matrix | Get adjacency matrix
get_adjacency_matrix.network | Get adjacency matrix
get_adjacency_matrix.network_module | Get adjacency matrix
get_association_matrix | Get association matrix
get_association_matrix.default | Get association matrix
get_association_matrix.matrix | Get association matrix
get_association_matrix.network | Get association matrix
get_association_matrix.network_module | Get association matrix
get_degree_distribution | Get the degree distribution for a network.
get_edge_weights_from_module | Get edge weights.
get_layout_for_modules | Internal function used to create coordinates based on a set of modules
get_network_arguments | Internal function used to extract 'network' objects from argument list.
get_network_characteristics | Characteristics of the network topology
get_network_modules | Get a list of modules from the network
get_node_names | Get node names
get_node_names.default | Get node names
get_node_names.matrix | Get node names
get_node_names.network | Get node names
get_node_names.network_module | Get node names
get_sigma | Get the covariance matrix
get_sigma.default | Get the covariance matrix
get_sigma.matrix | Get the covariance matrix
get_sigma.network | Get the covariance matrix
get_sigma.network_module | Get the covariance matrix
get_summary_for_node | Get summary for a node in the network.

## -- H --

heatmap_network | Plot heatmap representation of a network

## -- I --

is_PD | Internal function to check if a matrix is positive definite
is_symmetric_cpp | C++ implementation to check if a matrix is symmetric
is_weighted | Check if an object is weighted
is_weighted.default | Check if an object is weighted
is_weighted.matrix | Check if an object is weighted
is_weighted.network | Check if an object is weighted
is_weighted.network_module | Check if an object is weighted

## -- P --

perturb_network | Perturbs the connections in a network
plot.network | Plot function for 'network' object
plot.network_module | Plot function for 'network_module' object.
plot.network_plot | Plot function for 'network_plot' class
plot_gene_pair | Scatter plot of two gene expressions
plot_modules | Visualize a network and its modules
plot_network | Visualize a network
plot_network_diff | Plot the difference between two networks
plot_network_sim | Plot the similarity between two networks
print.network | Print function for 'network' object.
print.network_module | Print function for 'network_module' object.
print.network_plot | Print function for 'network_plot' class
pzinb | The Zero-Inflated Negative Binomial Distribution

## -- Q --

qzinb | The Zero-Inflated Negative Binomial Distribution

## -- R --

random_module | Create a random module
random_module_structure | Create a random network structure for a module
random_network | Create a network object.
reference | RNA-seq reference dataset
remove_connections | Remove connections in a network
remove_connections.default | Remove connections in a network
remove_connections.matrix | Remove connections in a network
remove_connections.network | Remove connections in a network
remove_connections.network_module | Remove connections in a network
remove_connections_to_node | Remove connections to a node
remove_connections_to_node.default | Remove connections to a node
remove_connections_to_node.matrix | Remove connections to a node
remove_connections_to_node.network | Remove connections to a node
remove_connections_to_node.network_module | Remove connections to a node
remove_weights | Removes the weights of all connections
remove_weights.default | Removes the weights of all connections
remove_weights.matrix | Removes the weights of all connections
remove_weights.network | Removes the weights of all connections
remove_weights.network_module | Removes the weights of all connections
replace_module_in_network | Internal function for replacing a module in the network
rewire_connections | Rewire connections
rewire_connections.default | Rewire connections
rewire_connections.matrix | Rewire connections
rewire_connections.network | Rewire connections
rewire_connections.network_module | Rewire connections
rewire_connections_to_node | Rewire connections to a node
rewire_connections_to_node.default | Rewire connections to a node
rewire_connections_to_node.matrix | Rewire connections to a node
rewire_connections_to_node.network | Rewire connections to a node
rewire_connections_to_node.network_module | Rewire connections to a node
ring_lattice_cpp | C++ implementation for creating a ring lattice
rzinb | The Zero-Inflated Negative Binomial Distribution

## -- S --

sample_link_nodes | Sample link nodes for new module
sample_module_nodes | Sample nodes for new module
sample_reference_data | Sample genes from reference dataset
set_module_edges | Internal function used to set the edges in a module
set_module_name | Set the name for a module
set_module_weights | Internal function to set the connection weights for a module
set_node_names | Set the node names in a network

## -- U --

update_module_with_random_weights | Generate small-world network structure for module