MS_shortestPaths: Calculate shortest paths

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

Description

This function calculates the shortest path(s) between any two reachable nodes of a network-table.

Usage

MS_shortestPaths(network_table, source_node, target_node, mode = "out",
                 type = "first")

Arguments

network_table	three-column matrix where each row represents and edge between two nodes. See function "MS_keggNetwork( )".
source_node	character vector containing the node from which the shortest paths will be calculated.
target_node	character vector containing the node to which the shortest path will be calculated.
mode	character constant indicating whether a directed or an undirected network will be considered. "all" indicates that all the edges of the network will be considered as undirected. "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 metabolite, which will be considered as undirected. The difference between the "out" and "SP" options, is that the latter aids reaching target metabolites that are substrate of irreversible reactions.
type	indicates whether all shortest paths or a single shortest path will be considered when there are several shortest paths between the source_node and the 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. Using type = "bw" increases the time required to compute this function.

Value

A vector or a matrix where each row contains a shortest path from the source_node to the target_node. KEGG IDs can be transformed into common names using the function "MS_changeNames( )".

References

G. Csardi and T. Nepusz (2015). igraph package, The Comprehensive R Archive Network, v1.0.1.

Examples

data(MetaboSignal_table)

# Shortest path from HK ("K00844") to a-D-Glucose ("cpd:C00267")

path1 <- MS_shortestPaths(MetaboSignal_table, "K00844", "cpd:C00267", mode = "SP")
path2 <- MS_shortestPaths(MetaboSignal_table, "K00844", "cpd:C00267", mode = "out")

# Shortest paths from G6PC ("K01084") to pyruvate ("cpd:C00022")

path3 <- MS_shortestPaths(MetaboSignal_table, "K01084", "cpd:C00022", type = "all")
path4 <- MS_shortestPaths(MetaboSignal_table, "K01084", "cpd:C00022", type = "bw")

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