createPathwayGraphs {CHRONOS} | R Documentation

## Convert KEGG Pathways to Gene-Gene Network Graphs.

### Description

Convert KEGG Pathways to Gene-Gene Network Graphs.

### Usage

    createPathwayGraphs(org, pathways, edgeTypes, doubleEdges, choice, groupMode)

### Arguments

`org` | KEGG organism identifier.
`pathways` | Vector of KEGG pathway identifiers.
`edgeTypes` | Vector of edge types mappings.
`doubleEdges` | Specify which edgeTypes should be considered bidirectional.
`choice` | Create metabolic graph either by using relations or reactions from KGML file ('reactions', 'relations')
`groupMode` | 'expand' to consider each group member a node, or 'collapse' to consider all components' genes as a node

### Details

KEGG pathways consist of nodes each one containing one or more genes. Thus, two kinds of adjacency matrices are created. The compact adjacency matrix retains the groupings and stores edge types between genes and genes, genes and groups of genes or between group of genes. The expanded adjacency matrix stores edge type information between individual genes.

### Value

A list containing a list of compact adjacency matrices, a list of expanded adjacency matrices, and list detailing all nodes, edges and interaction types.

### References

Li, C., Han, J., Yao, Q., Zou, C., Xu, Y., Zhang, C., ... & Li, X. (2013). Subpathway-GM: identification of metabolic subpathways via joint power of interesting genes and metabolites and their topologies within pathways. Nucleic acids research, 41(9), e101-e101.

### Examples

    # Download Insulin Signaling Pathway
    pathways <- c('04915', '04917', '04930', '05031')
    paths    <- downloadPathways(org='hsa', pathways=pathways)

    # Create pathway graph
    graphs   <- createPathwayGraphs(org='hsa', pathways=paths)

[Package CHRONOS version 1.12.0 Index]