keggDF2graph {keggorth}R Documentation

create a graph from a specific data frame format for KEGG orthology

Description

create a graph from a specific data frame format for KEGG orthology

Usage

keggDF2graph(df, root="KO.June07root")
data(KOgraph)

Arguments

df the data frame
root a name for root node

Details

the obvious directed graph structure from root to leaf nodes (pathway names) is instantiated for the orthology, nodeData attribute tag is loaded with the numerical tag for the term in KEGG, and nodeData attribute depth is loaded with depth from root

Value

a graphNEL-class instance

Note

This is only a support function. The graph is serialized in the package data directory.

Author(s)

Vince Carey <stvjc@channing.harvard.edu>

Examples

data(keggOrthDF)
keggOrthDF[1:5,]
data(KOgraph)
nodes(KOgraph)[1:4]
nodeData(KOgraph,,"tag")[1:5]
nodeData(KOgraph,,"depth")[1:5]

[Package keggorth version 1.2.0 Index]