% 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}}
}