combineKEGGnodes: Special treatment of nodes or edges for KEGG pathway...

In DGendooLab/pathviewM: a tool set for pathway based data integration and visualization

Description

combineKEGGnodes combines nodes into a group in a KEGG pathway graph. reaction2edge converts reactions into edges in KEGG pathway graph.

Usage

combineKEGGnodes(nodes, graph, combo.node)
reaction2edge(path, gR)

Arguments

nodes	character, names of the names to be combined.
graph, gR	a object of "graphNEL" class, the graph parsed and converted from KEGG pathway.
path	a object of "KEGGPathway" class, the parsed KEGG pathway.
combo.node	character, the name of result combined node.

Details

combineKEGGnodes not only combines nodes in the graph object, but also corresponding node data in the KEGG pathway object. This function is needed for KEGG-defined group nodes and parsed enzyme groups involved in the same reaction. reaction2edge converts a reaction into 2 consecutive edges between substrate and enzyme and enzyme and product. This function is needed as to faithfully show the compound-enzyme nodes and their interactions in Graphviz-style view of KEGG pathway.

Value

The results returned by combineKEGGnodes is a combined graph of "graphNEL" class. The results returned by reaction2edge is a list of 3 elements: gR, the converted graph ("graphNEL"); edata.new, the new edge data ("KEGGEdge"); ndata.new, the new node data ("KEGGNode").

Author(s)

Weijun Luo <[e-mail]>

References

Luo, W. and Brouwer, C., Pathview: an R/Bioconductor package for pathway based data integration and visualization. Bioinformatics, 2013, 29(14): 1830-1831, doi: 10.1093/bioinformatics/btt285

See Also

node.info the main parser function

DGendooLab/pathviewM documentation built on Dec. 17, 2021, 4 p.m.