man/keggPathwayGraphs.Rd
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 % Generated by roxygen2: do not edit by hand
 % Please edit documentation in R/keggDataREST.R
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 \name{keggPathwayGraphs}
 \alias{keggPathwayGraphs}
 \title{Download and parse KEGG pathway data}
 \usage{
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 keggPathwayGraphs(organism = "hsa", targRelTypes = c("GErel", "PCrel",
   "PPrel"), relPercThresh = 0.9, nodeOnlyGraphs = FALSE,
   updateCache = FALSE, verbose = TRUE)
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 }
 \arguments{
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 \item{organism}{organism code as defined by KEGG}
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 \item{targRelTypes}{target relation types}
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 \item{relPercThresh}{percentage of the number of relation types over all possible realtions in the pathway}
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 \item{nodeOnlyGraphs}{allow graphs with no edges}
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 \item{updateCache}{re-download KEGG data}
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 \item{verbose}{show progress of downloading and parsing}
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 }
 \value{
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 A list of \code{\link{graphNEL}} objects encoding the pathway information.
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 }
 \description{
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 Download and parse KEGG pathway data
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 }
 \examples{
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 # The pathway cache provided as part of the pathway contains only the 
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 # 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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 }
 \author{
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 Calin Voichita and Sorin Draghici
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 }
 \seealso{
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 \code{\link{keggPathwayNames}}
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 }