networkFromSif: Generate a network object.

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

Description

Generation of a list that contain all the global network information extracted from a sif file. When a subnetwork file is present, the information from the subnetwork is added to the list.

Usage

networkFromSif(netFileName, subNetFileName = NULL)

Arguments

netFileName	a character string for the name of file in SIF format that contains the information of the global network.
subNetFileName	a character string for the name of file in SIF format that contains the information of the subnetwork. This parameter is not mandatory. The information for the subnetwork is only extracted when a filename is given.

Value

a list containing the following components:

• netAll a hash containing all the information from the global network.

• nodesAll a vector of string representing all the nodes present in the global network.

• nodesSubNet a vector of string representing all the nodes present in the subnetwork to be tested or NULL when information not known.

Author(s)

Pascal Belleau, Astrid Deschenes

Examples

## Access SIF file for global network stored in subnetsim package
networkFile <- system.file("extdata", "demo_network.sif",
package="subnetsim")

## Create a network without the subnetwork information
demo_network <- subnetsim:::networkFromSif(netFileName = networkFile)

## Access SIF file for subnetwork stored in subnetsim package
subnetworkFile <- system.file("extdata", "demo_subnetwork.sif",
package="subnetsim")

## Create a network with the subnetwork information
demo_network_with_sub <- subnetsim:::networkFromSif(netFileName = networkFile,
    subNetFileName = subnetworkFile)

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