make_DM: Make a Duplication and Mutation Network

In langendorfr/netcom: NETwork COMparison Inference

Make a Duplication and Mutation Network

Description

Make an already existing network according to the Duplication and Mutation mechanism.

Usage

make_DM(size, net_kind, divergence, mutation, directed = FALSE)

Arguments

size	Number of nodes in the network.
net_kind	If the network is an adjacency matrix ("matrix") or an edge list ("list").
divergence	Probability that the new node loses edges associated with the node it duplicates. Needs to be between zero and one.
mutation	Probability that the new node gains edges not associated with the node it duplicates. Needs to be between zero and one.
directed	Binary variable determining if the network is directed, resulting in off-diagonal asymmetry in the adjacency matrix. Defaults to TRUE.

Details

Different from Duplication & Mutation models in that edges can only be lost.

Value

An adjacency matrix.

References

Ispolatov, I., Krapivsky, P. L., & Yuryev, A. (2005). Duplication-divergence model of protein interaction network. Physical review E, 71(6), 061911.

Examples

# Import netcom
library(netcom)

# Network size (number of nodes)
size <- 10

# Divergence parameter
divergence <- 0.237

# Mutation parameter
mutation <- 0.1

# Make network according to the Duplication & Mutation mechanism
make_DM(size = size, net_kind = "matrix", divergence = divergence, mutation = mutation)

langendorfr/netcom documentation built on July 23, 2022, 5:19 p.m.