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SDDE (version 1.0.1)

Shortcuts, Detours and Dead Ends (SDDE) Path Types in Genome Similarity Networks

Description

Compares the evolution of an original network X to an augmented network Y by counting the number of Shortcuts, Detours, Dead Ends (SDDE), equal paths and disconnected nodes.

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Version

Install

install.packages('SDDE')

Monthly Downloads

28

Version

1.0.1

License

GPL-3

Maintainer

Etienne Lord

Last Published

August 26th, 2015

Functions in SDDE (1.0.1)

load_network

is a helper function to load networks from files
complete_trace

return properties of a single path in two given networks (original and augmented, presented as undirected graphs) using a path analysis
info_node

returns additional information regarding the nodes of networks X and Y (original and augmented)
Sample_1

An original network X with 11 nodes and an augmented network Y of 14 nodes
g1

generic name for network X
Eukaryote_photo

An original and an augmented real genomic networks
Viruses

An original and an augmented real genomic networks
sample_path

is a helper function that creates a vector of non-repeating pathways to investigate
Eukaryote_nonphoto

An original and an augmented real genomic networks
info_network

returns additional information regarding the networks X and Y (original and augmented).
complete_network

compare two given networks (original and augmented, presented as undirected graphs) using a path analysis
random_network

creates random augmented networks X and Y
Plasmids

An original and an augmented real genomic networks
g2

generic name for network Y
SDDE.version

Version information.
save_network_big

Helper function to save an illustration of a network to file with more than 50 nodes.
plot_network

Helper function to display an illustration of a network.
SDDE-package

Shortcuts, Detours and Dead Ends (SDDE) Path Types in Genome Similarity Networks
save_network

is an helper function to save an illustration of a network into a file
complete_restart

compares two given networks (original and augmented, presented as undirected graphs) using a path analysis
Sample_2

An network X of 6 nodes and an augmented network Y with 7 nodes
sample_network

compares two networks using a path analysis of total pathways