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SeqNet

An R package for simulating RNA-seq counts from gene-gene association networks.

Installation

SeqNet can be installed from CRAN or from GitHub using the devtools package:

# From CRAN:
install.packages('SeqNet')

# From GitHub:
# install.packages('devtools')
devtools::install_github('tgrimes/SeqNet')

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Version

Install

install.packages('SeqNet')

Monthly Downloads

49

Version

1.1.3

License

GPL-2 | GPL-3

Maintainer

Tyler Grimes

Last Published

July 9th, 2021

Functions in SeqNet (1.1.3)

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.

create_empty_module

Create a module

components_in_adjacency

C++ implementation to obtain connected components in a graph.

as_single_module

Collapses all modules in network into a single module

add_modules_to_network

Internal function for adding a set of modules to the network

connect_module_structure

Connect disconnected components in an adjacency matrix

create_cytoscape_file

Create an edge table file for Cytoscape

check_adjacency_cpp

C++ implementation to check if a matrix is an adjacency matrix

all_networks_contain_same_nodes

Internal function to check if a list of networks all contain the same nodes.

create_module_from_association_matrix

Create a module from an association matrix

create_network_from_association_matrix

Create a network object from an association matrix

create_network_from_adjacency_matrix

Create a network object from an adjacency matrix

create_empty_network

Create a network object.

gen_partial_correlations

Generate partial correlations for a list of networks.

Generate RNA-seq data from an underlying network

est_params_from_reference

Estimate ZINB parameters from reference data

create_modules_for_network

Randomly sample subsets of genes for each module

Generate observations from a Gaussian graphical model.

get_layout_for_modules

Internal function used to create coordinates based on a set of modules

get_edge_weights_from_module

Get edge weights.

get_association_matrix

Get association matrix

get_association_matrix.default

Get association matrix

get_network_modules

Get a list of modules from the network

get_node_names.network

get_node_names.network_module

C++ implementation of empirical CDF

get_adjacency_matrix

Get adjacency matrix

edges_from_adjacency_cpp

C++ implementation for obtaining an edge list from adjacency matrix

Generate ZINB counts from an underlying network

get_network_characteristics

Characteristics of the network topology

get_network_arguments

Internal function used to extract 'network' objects from argument list.

create_network_from_modules

Create a network object.

The Zero-Inflated Negative Binomial Distribution

get_node_names.default

get_sigma.network_module

Get the covariance matrix

is_weighted.network

Check if an object is weighted

get_sigma.network

Get the covariance matrix

Plot function for 'network' object

Internal function to check if a matrix is positive definite

heatmap_network

Plot heatmap representation of a network

perturb_network

Perturbs the connections in a network

get_sigma.matrix

Get the covariance matrix

get_adjacency_matrix.network_module

Get adjacency matrix

get_adjacency_matrix.network

Get adjacency matrix

get_association_matrix.matrix

Get association matrix

get_summary_for_node

Get summary for a node in the network.

get_adjacency_matrix.default

Get adjacency matrix

remove_connections.network_module

Remove connections in a network

plot_network_sim

Plot the similarity between two networks

Get the covariance matrix

is_weighted.default

Check if an object is weighted

get_association_matrix.network

Get association matrix

get_sigma.default

Get the covariance matrix

remove_connections_to_node

Remove connections to a node

Print function for 'network' object.

is_weighted.matrix

Check if an object is weighted

The Zero-Inflated Negative Binomial Distribution

rewire_connections.matrix

Rewire connections

rewire_connections

Rewire connections

is_symmetric_cpp

C++ implementation to check if a matrix is symmetric

remove_connections.matrix

Remove connections in a network

Create a random module

Check if an object is weighted

get_node_names.matrix

random_module_structure

Create a random network structure for a module

remove_connections.network

Remove connections in a network

The Zero-Inflated Negative Binomial Distribution

Scatter plot of two gene expressions

remove_weights.network

Removes the weights of all connections

remove_connections.default

Remove connections in a network

remove_connections_to_node.network

Remove connections to a node

remove_connections_to_node.network_module

Remove connections to a node

Visualize a network and its modules

remove_weights.matrix

Removes the weights of all connections

sample_link_nodes

Sample link nodes for new module

remove_connections_to_node.default

Remove connections to a node

remove_connections

Remove connections in a network

is_weighted.network_module

Check if an object is weighted

plot.network_module

Plot function for 'network_module' object.

Set the node names in a network

update_module_with_random_weights

Generate small-world network structure for module

sample_module_nodes

Sample nodes for new module

rewire_connections.network

Rewire connections

get_degree_distribution

Get the degree distribution for a network.

get_association_matrix.network_module

Get association matrix

Create a network object.

plot_network_diff

Plot the difference between two networks

Visualize a network

get_adjacency_matrix.matrix

Get adjacency matrix

plot.network_plot

Plot function for 'network_plot' class

print.network_plot

Print function for 'network_plot' class

print.network_module

Print function for 'network_module' object.

sample_reference_data

Sample genes from reference dataset

set_module_edges

Internal function used to set the edges in a module

remove_weights.network_module

Removes the weights of all connections

remove_connections_to_node.matrix

Remove connections to a node

rewire_connections_to_node

Rewire connections to a node

rewire_connections.network_module

Rewire connections

ring_lattice_cpp

C++ implementation for creating a ring lattice

remove_weights.default

Removes the weights of all connections

Removes the weights of all connections

RNA-seq reference dataset

The Zero-Inflated Negative Binomial Distribution

rewire_connections.default

Rewire connections

rewire_connections_to_node.matrix

Rewire connections to a node

rewire_connections_to_node.default

Rewire connections to a node

replace_module_in_network

Internal function for replacing a module in the network

rewire_connections_to_node.network

Rewire connections to a node

set_module_name

Set the name for a module

rewire_connections_to_node.network_module

Rewire connections to a node

set_module_weights

Internal function to set the connection weights for a module

create_module_from_adjacency_matrix

Create a module from an adjacency matrix