Description Usage Arguments Value Author(s) See Also Examples
Download and parse KEGG pathway data
1 2 3 | 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
1 2 3 4 5 6 7 8 9 10 11 12 13 14 | # 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"]]))
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