MS_distances: Calculate gene-metabolite distance matrix

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

Description

This function generates a distance matrix containing the length of all shortest paths from a set of genes (or reactions) to a set of metabolites. The shortest path length between two nodes is defined as the minimum number of edges between these two nodes.

Usage

MS_distances(network_table, organism_code, mode = "SP", source_genes = "all",
             target_metabolites = "all", names = FALSE)

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( )".
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 the "SP" options, is that the latter aids reaching target metabolites that are substrates of irreversible reactions.
source_genes	character vector containing the genes from which the shortest paths will be calculated. Remember that Entrez IDs or gene symbols can be transformed into KEGG IDs using the function "MS_convertGene( )". By default, source_genes = "all", indicating that all the genes of the network will be used.
target_metabolites	character vector containing the KEGG IDs of the metabolites to which the shortest paths will be calculated. Compound KEGG IDs can be obtained using the function "MS_keggFinder( )". By default, target_metabolites = "all", indicating that all the metabolites of the network will be used.
names	logical scalar indicating whether metabolite or gene KEGG IDs will be transformed into common metabolite names or gene symbols. Reaction IDs remain unchanged.

Value

A matrix containing the shortest path length from the genes or reactions (in the rows) to the metabolites (in the columns). For unreacheable metabolites Inf is included.

References

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

Examples

data(MetaboSignal_table)

# Distances from Ship2 (65038) and Ppp2r5b (309179) to D-glucose ("cpd:C00031")

MS_convertGene(genes = c("65038","309179"), "rno", "rat", output = "matrix")

distances_targets <- MS_distances(MetaboSignal_table, organism_code = "rno",
                                  source_genes = c("K15909", "K11584"),
                                  target_metabolites = "cpd:C00031",
                                  names = TRUE)

# Distances from all genes to all metabolites of the network

distances_all <- MS_distances(MetaboSignal_table, organism_code = "rno")

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