keggPathwayGraphs {ROntoTools} | R Documentation |
Download and parse KEGG pathway data
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
# 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"]]))