% Generated by roxygen2: do not edit by hand
 % Please edit documentation in R/keggDataREST.R

 \name{keggPathwayGraphs}
 \alias{keggPathwayGraphs}
 \title{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{

 \item{organism}{organism code as defined by KEGG}

 \item{targRelTypes}{target relation types}

 \item{relPercThresh}{percentage of the number of relation types over all possible realtions in the pathway}

 \item{nodeOnlyGraphs}{allow graphs with no edges}

 \item{updateCache}{re-download KEGG data}

 \item{verbose}{show progress of downloading and parsing}

 }
 \value{

 A list of \code{\link{graphNEL}} objects encoding the pathway information.

 }
 \description{

 Download and parse KEGG pathway data

 }
 \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"]]))

 }
 \author{

 Calin Voichita and Sorin Draghici

 }
 \seealso{

 \code{\link{keggPathwayNames}}

 }