MWAS_KEGG_network: Build a KEGG-based metabolic network

In MWASTools: MWASTools: an integrated pipeline to perform metabolome-wide association studies

Description

This function generates a KEGG-based metabolic network connecting substrate-product pairs. The network is formated as a four-column matrix, where each row represents an edge connecting two metabolites (from metabolite in column 1 to metabolite in column 2). The third column contains the identifiers (IDs) of the reactions performing each of the metabolic conversions, while the fourth column indicates the direction of each reaction.

Usage

MWAS_KEGG_network(kegg_paths = NULL)

Arguments

kegg_paths

character vector containing the KEGG IDs of the metabolic pathways of interest (organism-specific). For example, the KEGG ID for the human "glycolysis/gluconeogenesis" pathway is"hsa00010". By default, the KEGG IDs contained in the dataset "KEGG_metabolic_paths" will be used.

Value

A four-column matrix where each row represents an edge between two nodes.

Note

Like in the MetaboSignal package, reaction directionality has been cross-checked and corrected (when required) based on previous literature (Duarte et al., 2007).

References

Duarte NC, et al. (2007). Global reconstruction of the human metabolic network based on genomic and bibliomic data. Proceedings of the National Academy of Sciences, 104, 1777-1782.

Posma JM, et al. (2014). MetaboNetworks, an interactive Matlab-based toolbox for creating, customizing and exploring sub-networks from KEGG. Bioinformatics, 30, 893-895.

Rodriguez-Martinez A, et al. (2017).MetaboSignal: a network-based approach for topological analysis of metabotype regulation via metabolic and signaling pathways. Bioinformatics, 33, 773-775.

Zhang JD, Wiemann S. (2009). KEGGgraph: a graph approach to KEGG PATHWAY in R and Bioconductor. Bioinformatics, 25, 1470-1471.

http://www.kegg.jp/kegg/docs/keggapi.html

Examples

## Define the paths that will be used to build the network
data(KEGG_metabolic_paths)
metabo_paths =  KEGG_metabolic_paths[[1]][, 1]

## Build metabolic network-table: might take few minutes
metabolic_network = MWAS_KEGG_network(kegg_paths = metabo_paths)

MWASTools documentation built on Nov. 8, 2020, 5:07 p.m.