Man pages for tgrimes/SeqNet
Generate RNA-Seq Data from Gene-Gene Association Networks
| 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... |
| all_networks_contain_same_nodes | Internal function to check if a list of networks all contain... |
| as_single_module | Collapses all modules in network into a single module |
| 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_module_from_adjacency_matrix | Create a module from an adjacency matrix |
| create_module_from_association_matrix | Create a module from an association matrix |
| create_modules_for_network | Randomly sample subsets of genes for each module |
| create_network_from_adjacency_matrix | Create a network object from adjacency matrix |
| create_network_from_association_matrix | Create a network object from an association matrix |
| create_network_from_modules | Create a network object. |
| dzinb | The Zero-Inflated Negative Binomial Distribution |
| ecdf_cpp | C++ implementation of empirical CDF |
| edges_from_adjacency_cpp | C++ implementation for obtaining an edge list from adjacency... |
| est_params_from_reference | Estimate ZINB parameters from reference data |
| 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... |
| get_network_arguments | Internal function used to extract 'network' objects from... |
| 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. |
| heatmap_network | Plot heatmap representation of a network |
| is_adjacency_cpp | C++ implementation to check if a matrix is an adjacency... |
| 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 |
| perturb_network | Perturbs the connections in a network |
| plot_gene_pair | Scatter plot of two gene expressions |
| plot_modules | Visualize a network and its modules |
| plot_network | Visualize a network |
| plot.network | Plot function for 'network' object |
| plot_network_diff | Plot the difference between two networks |
| plot.network_module | Plot function for 'network_module' object. |
| plot.network_plot | Plot function for 'network_plot' class |
| 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 |
| qzinb | The Zero-Inflated Negative Binomial Distribution |
| 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 |
| 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 |
| update_module_with_random_weights | Generate small-world network structure for module |
