ROntoTools (version 2.0.0)

keggPathwayGraphs: Download and parse KEGG pathway data

Description

Download and parse KEGG pathway data

Usage

keggPathwayGraphs(organism = "hsa", targRelTypes = c("GErel", "PCrel", "PPrel"), relPercThresh = 0.9, nodeOnlyGraphs = FALSE, updateCache = FALSE, verbose = TRUE)

Arguments

organism

organism code as defined by KEGG

targRelTypes

target relation types

relPercThresh

percentage of the number of relation types over all possible realtions in the pathway

nodeOnlyGraphs

allow graphs with no edges

updateCache

re-download KEGG data

verbose

show progress of downloading and parsing

Value

A list of graphNEL objects encoding the pathway information.

See Also

keggPathwayNames

Examples

# The pathway cache provided as part of the pathway contains only the 
# pathways that passed the default filtering. We recommend, re-downloading
# the pathways using the updateCache parameter
kpg <- keggPathwayGraphs("hsa")

# to update the pathway cache for human run:
# kpg <- keggPathwayGraphs("hsa", updateCache = TRUE)
# this is time consuming and depends on the available bandwith.

head(names(kpg))

kpg[["path:hsa04110"]]
head(nodes(kpg[["path:hsa04110"]]))
head(edges(kpg[["path:hsa04110"]]))