SDDE-package: Shortcuts, Detours and Dead Ends (SDDE) Path Types in Genome...

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

Description

SDDE compares the evolution of an original network X to an augmented network Y by counting the number of shortcuts, detours, dead ends, equal paths and disconnected nodes.

Four different types of paths in Y that pass by at least one augmented node (i.e. a node that exists in Y but not in X) can be defined as follows:

1) Shortcut is a path between two nodes, originally present in X, that is shorter in Y than in X.

2) Detour is a path such that it connects two nodes originally present in X and is longer in Y than in X.

3) Dead End is a path that exists in X, but is impossible in Y.

4) Equal is a path that has the same length in X an Y.

The numbers of disconnected nodes is also reported.

Details

Package:	SDDE
Type:	Package
Version:	1.0.1
Date:	2015-08-20
License:	GPL-2
Maintainer:	Etienne Lord <[e-mail]>,
	François-Joseph Lapointe <[e-mail]>

Function complete_network computes the number of paths in each category.

Function complete_restart is similar to the complete_network function but it identifies the paths in a predefined order.

Function complete_trace is similar to the complete_network function but allow the enumeration of nodes and taxa in a path.

Function sample_network computes the number of paths in each category for a given set of nodes of the original network X.

Function random_network creates a random network X and an augmented network Y using Erdos-Renyi or Barabási–Albert models.

Function save_network and codeplot_network creates rendering of network X and network Y in various file formats (svg, png and eps).

Function load_network loads a network from a list of edges (tab-separated) which is compatible with the complete_network, complete_restart and sample_network function.

Author(s)

Etienne Lord, Margaux Le Cam, Éric Bapteste, Vladimir Makarenkov and François-Joseph Lapointe

See Also

complete_network, complete_restart, complete_trace, sample_network, load_network, save_network plot_network

SDDE documentation built on May 1, 2019, 9:01 p.m.