MS_shortestPathsNetwork: Build shortest-path subnetwork

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

Description

This function allows calculating the shortest paths from a set of source nodes to a set of target nodes, and representing them as a network. By default, the function exports 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: signaling-gene, metabolic-gene, reaction or compound. The second attribute file allows highlighting the source and target nodes.

Usage

MS_shortestPathsNetwork(network_table, organism_code, source_nodes, target_nodes,
                        mode = "out", type = "first", distance_th = Inf, names = TRUE,
                        export_cytoscape = TRUE, file_name = "MS")

Arguments

network_table	three-column matrix where each row represents an edge between two nodes. See function "MS_keggNetwork( )".
organism_code	character vector containing the KEGG code for the organism of interest. For example the KEGG code for the rat is "rno". See the function "MS_keggFinder( )".
source_nodes	character vector containing the node IDs (typically genes) from which the shortest paths will be calculated. When using gene IDs make sure that they are consistent with the format of the network (i.e. organism-specific gene IDs or orthology IDs). Remember that Entrez IDs and gene symbols can be transformed into KEGG IDs with the function "MS_convertGene( )".
target_nodes	character vector containing the nodes IDs (typically compounds) to which the shortest paths will be calculated. Compound KEGG IDs can be obtained using the function "MS_keggFinder( )".
mode	character constant indicating whether a directed (mode = "out") or semi-directed (mode = "SP") network will be considered. "out" indicates that all the edges of the network will be considered as directed. "SP" indicates that all network will be considered as directed except the edges linked to target_node, which will be considered as undirected. The difference between the "out" and the "SP" options, is that the latter aids reaching target metabolites that are substrates of irreversible reactions.
type	character constant indicating whether all shortest paths or a single shortest path will be considered when there are several shortest paths between a source node and a target node. If type = "all", all shortest paths will be considered. If type = "first" a single path will be considered. If type = "bw" the path with the highest betweenness score will be considered. The betweenness score is calculated as the average betweenness of the gene nodes of the path. Note that using type = "bw" increases the time required to compute this function.
distance_th	establishes a shortest path length threshold. Only shortest paths with length below this threshold will be included in the network.
names	logical scalar indicating whether metabolite or gene KEGG IDs will be transformed into common metabolite names or gene symbols. Reaction IDs remain unchanged.
export_cytoscape	logical scalar indicating whether network and attribute Cytoscape files will be generated and exported.
file_name	character vector that allows customizing the name of the exported files.

Value

A matrix where each row represents an edge between two nodes. By default, the function also generates 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.

Note

The network-table generated with this function can be also visualized in R using the igraph package. The network-table can be transformed into an igraph object using the function "graph.data.frame( )" from igraph.

References

Csardi, G. & Nepusz, T. (2006). The igraph software package for complex network research. InterJournal, Complex Systems, 1695.

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)

# Shortest paths from G6PC ("K01084") to pyruvate ("cpd:C00022") and
# to a-D-Glucose ("cpd:C00267")

subnet_first <- MS_shortestPathsNetwork(MetaboSignal_table, organism_code = "rno",
                                        source_nodes = "K01084",
                                        target_nodes = c("cpd:C00022", "cpd:C00267"),
                                        mode = "SP", type = "first")

subnet_all <- MS_shortestPathsNetwork(MetaboSignal_table, organism_code = "rno",
                                      source_nodes = "K01084",
                                      target_nodes = c("cpd:C00022", "cpd:C00267"),
                                      mode = "SP", type = "all")

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