git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/DEGraph@59368 bc3139a8-67e5-0310-9ffc-ced21a209358
Pierre Neuvial authored on 17/10/2011 21:22:04 git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/DEGraph@50237 bc3139a8-67e5-0310-9ffc-ced21a209358
Nishant Gopalakrishnan authored on 15/10/2010 18:54:36 | 1 | 1 |
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+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% |
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+% Do not modify this file since it was automatically generated from: |
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+% |
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+% ./getKEGGPathways.R |
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+% |
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+% by the Rdoc compiler part of the R.oo package. |
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+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% |
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+ |
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+\name{getKEGGPathways}
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+\alias{getKEGGPathways}
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+ |
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+ |
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+\title{Builds a graph for each of the KEGG pathways}
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+ |
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+\description{
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+ Builds a graph for each of the KEGG pathways. |
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+} |
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+ |
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+\usage{getKEGGPathways(path=NULL, rootPath="networkData/ftp.genome.jp/pub/kegg/xml/kgml", organism="hsa", metaTag=c("non-metabolic", "metabolic"), pattern=NULL, verbose=FALSE)}
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+ |
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+\arguments{
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+ \item{path}{A \code{\link[base]{character}} value, the local _full_ path of KGML data.}
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+ \item{rootPath}{A \code{\link[base]{character}} value, the local _root_ path of KGML data.}
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+ \item{organism}{A \code{\link[base]{character}} value specifying the organism whose
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+ pathways should be considered. Defaults to "hsa" (Homo Sapiens).} |
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+ \item{metaTag}{A \code{\link[base]{character}} value, specifying the type of pathways to
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+ be considered ("metabolic" or "non-metabolic"). Defaults to "non-metabolic".}
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+ \item{pattern}{An optional \code{\link[base]{character}} value specifying a file name pattern to
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+ look for.} |
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+ \item{verbose}{If \code{\link[base:logical]{TRUE}}, extra information is output.}
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+} |
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+ |
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+\value{
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+ A \code{\link[base]{list}} containing a \code{\link[=graph-class]{graph}} object for each KEGG pathway with at least one edge.
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+} |
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+ |
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+\details{If 'path' is supplied, KGML files in this directory are loaded.
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+ Otherwise, KGML files are assumed to be in |
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+ <rootPath>/<metaTag>/"organisms"/<organism>, which mirrors the |
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+ structure of the KEGG KGML file repository. |
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+} |
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+ |
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+\author{Laurent Jacob, Pierre Neuvial and Sandrine Dudoit}
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+ |
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+\seealso{
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+ \code{\link{parseKGML}}
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+ \code{\link{KEGGpathway2Graph}}
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+} |
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+ |
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+\examples{
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+library("KEGGgraph")
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+ |
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+## example of KGML files |
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+path <- system.file("extdata", package="KEGGgraph")
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+grList <- getKEGGPathways(path=path, verbose=TRUE) |
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+print(grList) |
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+ |
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+graph <- grList[[1]] |
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+plotKEGGgraph(graph) |
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+ |
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+\dontrun{
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+ ## Download all human KGML pathways locally |
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+ pathname <- system.file("downloadScripts", "downloadKeggXmlFiles.R", package="DEGraph")
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+ source(pathname) |
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+ |
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+ ## Load some of them |
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+ grList <- getKEGGPathways(pattern="040", verbose=TRUE) |
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+ print(grList) |
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+ |
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+ graph <- grList[[1]] |
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+ plotKEGGgraph(graph) |
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+} |
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+} |
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+ |