MS_exportCytoscape: Export network in cytoscape format

In MetaboSignal: MetaboSignal: a network-based approach to overlay and explore metabolic and signaling KEGG pathways

Description

This function generates a network file and two attribute files ("NodesType.txt", "TargetNodes.txt"), which can be imported into Cytoscape to visualize the network. The first attribute file allows customizing the nodes of the network based on the molecular entity they represent: compound, reaction, metabolic-gene or signaling-gene. The second attribute file allows highlighting a set of nodes of interest.

Usage

MS_exportCytoscape(network_table, organism_code, names = TRUE,
                   targets = NULL, file_name = "MS")

Arguments

network_table	three-column matrix where each row represents and edge between two nodes. Nodes must be KEGG IDs, not common names. See function "MS_keggNetwork()". For human networks, Entrez gene IDs are also allowed.
organism_code	character vector containing the KEGG code for the organism of interest. For example the KEGG code for the rat is "rno". See function "MS_keggFinder( )".
names	logical scalar indicating whether metabolite or gene KEGG IDs will be transformed into common metabolite names or gene symbols. Reaction IDs remain unchanged.
targets	optional character vector containing the IDs of the target nodes to be discriminated from the other nodes of the network.
file_name	character vector that allows customizing the name of the exported files.

Value

A data frame where each row represents an edge between two nodes (from source to target). The function also generates and exports a network file ("MS_Network.txt") and two attribute files ("MS_NodesType.txt", "MS_TargetNodes.txt"), which can be imported into Cytoscape to visualize the network.

References

Shannon P et al. (2003). Cytoscape: a software environment for integrated models of biomolecular interaction networks. Genome Research, 13, 2498-2504.

Examples

data(MetaboSignal_table)
MS_exportCytoscape(MetaboSignal_table, organism_code = "rno", names = FALSE)

MetaboSignal documentation built on Nov. 8, 2020, 6 p.m.