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SDDE (version 1.0.0)

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

1.0.0

License

GPL-3

Maintainer

Etienne Lord

Last Published

March 6th, 2015

Functions in SDDE (1.0.0)

complete_trace

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

An original and an augmented real genomic networks
complete_network

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

returns additional information regarding the networks X and Y (original and augmented).
g1

generic name for network X
save_network

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

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

creates random augmented networks X and Y
complete_restart

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

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

compares two networks using a path analysis of total pathways
SDDE-package

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

An original and an augmented real genomic networks
Sample_2

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

Helper function to save an illustration of a network to file with more than 50 nodes.
g2

generic name for network Y
Eukaryote_photo

An original and an augmented real genomic networks
load_network

is a helper function to load networks from files
Sample_1

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

An original and an augmented real genomic networks