CHRONOS (version 1.0.3)

createPathwayGraphs: 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

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.

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.

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)