simuleSubNet: Generating simulated subnetworks.

In belleau/subnetsim: Validating that a specific subnetwork has significantly more interactions than expected by randomness

Description

Generationg multiple simulated sub-networks from a network. All subnetworks have the same number of nodes.

Usage

simuleSubNet(netAll, nodesAll, nbIter, nbNodes, seedV)

Arguments

netAll	a hash representing the global network.
nodesAll	list of character string representing all the nodes in the global network.
nbIter	a single integer indicating the number of iterations to be run.
nbNodes	a integer indicating the number of nodes that each simulated sub-network will contain.
seedV	a integer, a seed used when reproducible results are needed. When a value inferior or equal to zero is given, a random integer is used.

Value

a data.frame containing the information from all simulated subnetworks. Each row of the data.frame corresponds to one simulation:

• nbLink: Number of links in the simulated subnetworks

• nbNodesOneLink: Number of nodes of the simulated subnetworks including the first-degree neighbor nodes.

• nbLinkOneLink Number of links of the simulated subnetworks including all the links from the first-degree neighbor nodes.

Author(s)

Pascal Belleau, Astrid Deschenes

Examples

# Access demo files stored in the subnetsim package
networkFile <- system.file("extdata", "demo_network.sif", package="subnetsim")
subnetworkFile <- system.file("extdata", "demo_subnetwork.sif", package="subnetsim")

# Load a global network and its tested subnetwork using SIF format files
demo_network_with_sub <- network(netFileName = networkFile,
    subNetFileName = subnetworkFile)

# Run simulation
simulatedSubnetwork <- subnetsim:::simuleSubNet(netAll = demo_network_with_sub$netAll,
    nodesAll = demo_network_with_sub$nodesAll,
    nbIter = 2, nbNodes <- length(demo_network_with_sub$nodesSubNet),
    seedV = 3122)

# To see a summary of the content of the "subnetwork" object
simulatedSubnetwork

belleau/subnetsim documentation built on May 27, 2019, 2:08 p.m.