MWAS_KEGG_network {MWASTools} | R Documentation

## Build a KEGG-based metabolic network

### 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)

[Package MWASTools version 1.11.0 Index]