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

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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.

Author
Etienne Lord, Margaux Le Cam, Eric Bapteste, Vladimir Makarenkov and Francois-Joseph Lapointe
Date of publication
2015-08-26 23:23:36
Maintainer
Etienne Lord <m.etienne.lord@gmail.com>
License
GPL-3
Version
1.0.1

View on CRAN

Man pages

complete_network
compare two given networks (original and augmented, presented...
complete_restart
compares two given networks (original and augmented,...
complete_trace
return properties of a single path in two given networks...
Eukaryote_nonphoto
An original and an augmented real genomic networks
Eukaryote_photo
An original and an augmented real genomic networks
g1
generic name for network X
g2
generic name for network Y
info_network
returns additional information regarding the networks X and Y...
info_node
returns additional information regarding the nodes of...
load_network
is a helper function to load networks from files
Plasmids
An original and an augmented real genomic networks
plot_network
Helper function to display an illustration of a network.
random_network
creates random augmented networks X and Y
Sample_1
An original network X with 11 nodes and an augmented network...
Sample_2
An network X of 6 nodes and an augmented network Y with 7...
sample_network
compares two networks using a path analysis of total pathways
sample_path
is a helper function that creates a vector of non-repeating...
save_network
is an helper function to save an illustration of a network...
save_network_big
Helper function to save an illustration of a network to file...
SDDE-package
Shortcuts, Detours and Dead Ends (SDDE) Path Types in Genome...
Version
Version information.
Viruses
An original and an augmented real genomic networks

Files in this package

SDDE
SDDE/src
SDDE/src/createSamplePath.c
SDDE/NAMESPACE
SDDE/NEWS
SDDE/data
SDDE/data/Eukaryote_nonphoto.rda
SDDE/data/Eukaryote_photo.rda
SDDE/data/Plasmids.rda
SDDE/data/Sample_2.rda
SDDE/data/datalist
SDDE/data/Sample_1.rda
SDDE/data/Viruses.rda
SDDE/R
SDDE/R/sample_network.R
SDDE/R/random_network.R
SDDE/R/version.R
SDDE/R/complete_network.R
SDDE/R/complete_network_trace.R
SDDE/R/load_network.R
SDDE/R/save_network.R
SDDE/R/info_network.R
SDDE/MD5
SDDE/DESCRIPTION
SDDE/man
SDDE/man/g2.Rd
SDDE/man/Sample_1.Rd
SDDE/man/load_network.Rd
SDDE/man/Version.Rd
SDDE/man/info_node.Rd
SDDE/man/plot_network.Rd
SDDE/man/info_network.Rd
SDDE/man/Plasmids.Rd
SDDE/man/Viruses.Rd
SDDE/man/sample_path.Rd
SDDE/man/complete_restart.Rd
SDDE/man/complete_network.Rd
SDDE/man/Eukaryote_nonphoto.Rd
SDDE/man/SDDE-package.Rd
SDDE/man/Eukaryote_photo.Rd
SDDE/man/g1.Rd
SDDE/man/Sample_2.Rd
SDDE/man/save_network_big.Rd
SDDE/man/random_network.Rd
SDDE/man/sample_network.Rd
SDDE/man/save_network.Rd
SDDE/man/complete_trace.Rd