Generate RNA-Seq Data from Gene-Gene Association Networks

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Documentation for package ‘SeqNet’ version 1.1.3

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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
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_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_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