keggPathwayGraphs: Download and parse KEGG pathway data
In ROntoTools: R Onto-Tools suite

Description Usage Arguments Value Author(s) See Also Examples

Download and parse KEGG pathway data

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

`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

A list of graphNEL objects encoding the pathway information.

Calin Voichita and Sorin Draghici

keggPathwayNames

# 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"]]))