@@ -16,7 +16,7 @@ Description: DEGraph implements recent hypothesis testing methods

   and tools to visualize the results.

 License: GPL-3

 LazyLoad: yes

-Imports: graph, KEGGgraph, lattice, mvtnorm, NCIgraph, R.methodsS3, RBGL, Rgraphviz, rrcov

-Suggests: corpcor, fields, graph, KEGGgraph, lattice, marray, NCIgraph, RBGL, rrcov, Rgraphviz

+Imports: graph, KEGGgraph, lattice, mvtnorm, R.methodsS3, RBGL, Rgraphviz, rrcov

+Suggests: corpcor, fields, graph, KEGGgraph, lattice, marray, RBGL, rrcov, Rgraphviz

 Depends: R (>= 2.10.0), R.utils

 biocViews: Microarray, Bioinformatics, DifferentialExpression, GraphsAndNetworks

@@ -25,4 +25,4 @@ importFrom(rrcov, T2.test)

 importFrom(mvtnorm, rmvnorm)

 importFrom(RBGL,connectedComp)

 importFrom(lattice, level.colors)

-importFrom(NCIgraph, is.NCIgraph)

+## importFrom(NCIgraph, is.NCIgraph)

new file mode 100644

@@ -0,0 +1,48 @@

+## Copyright 2011 Laurent Jacob

+

+## This file is part of DEGraph.

+

+## DEGraph is free software: you can redistribute it and/or modify

+## it under the terms of the GNU General Public License as published by

+## the Free Software Foundation, either version 3 of the License, or

+## (at your option) any later version.

+

+## DEGraph is distributed in the hope that it will be useful,

+## but WITHOUT ANY WARRANTY without even the implied warranty of

+## MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the

+## GNU General Public License for more details.

+

+## You should have received a copy of the GNU General Public License

+## along with DEGraph.  If not, see <http://www.gnu.org/licenses/>.

+

+#########################################################################/**

+# @RdocFunction is.NCIgraph

+##

+## @title "Assess whether a graph is a NCI graph"

+##

+##

+## \description{

+##  @get "title".

+## }

+##

+## @synopsis

+##

+## \arguments{

+##   \item{gr}{A \code{\link[=graph-class]{graph}} object.}

+## }

+##

+## \value{A @logical, @TRUE if the graph is a NCI graph, @FALSE otherwise.}

+##

+## @author

+##

+## \seealso{

+##   @see "parseNCInetwork"

+## }

+##

+##*/########################################################################

+

+is.NCIgraph <- function(gr)

+  {

+    ##(length(gr@nodeData@data) > 0) && (length(grep('biopax',names(gr@nodeData@data[[1]]))) > 0)

+    isTRUE(class(gr) == 'NCIgraph')

+  }

@@ -19,19 +19,17 @@ sourceDirectory(path)

 ## get all NCI pathways

 ## - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

-##library('NCIgraph')

-##path <- system.file("downloadScripts", package="NCIgraph")

-##sourceDirectory(path)

-##load(file.path('rawNCINetworks','NCI-cyList.RData'))

+## library('NCIgraph')

+path <- system.file("downloadScripts", package="NCIgraph")

+sourceDirectory(path)

+load(file.path('rawNCINetworks','NCI-cyList.RData'))

-##grList <- getNCIPathways(cyList=NCI.cyList, verbose=verbose)$pList

+grList <- getNCIPathways(cyList=NCI.cyList, verbose=verbose)$pList

 ## - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

 ## get all KEGG pathways

 ## - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

-

-grList <- getKEGGPathways(organism="hsa", metaTag="non-metabolic", verbose=verbose)

-

+## grList <- getKEGGPathways(organism="hsa", metaTag="non-metabolic", verbose=verbose)

 ## grList <- getKEGGPathways(organism="hsa", metaTag="non-metabolic", patt="04060", verbose=verbose)

 ## - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

new file mode 100644

@@ -0,0 +1,29 @@

+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

+% Do not modify this file since it was automatically generated from:

+% 

+%  ./is.NCIgraph.R

+% 

+% by the Rdoc compiler part of the R.oo package.

+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

+

+\name{is.NCIgraph}

+\alias{is.NCIgraph}

+

+

+\title{Assess whether a graph is a NCI graph}

+

+

+\description{

+ Assess whether a graph is a NCI graph.

+}

+

+\usage{is.NCIgraph(gr)}

+

+\arguments{

+  \item{gr}{A \code{\link[=graph-class]{graph}} object.}

+}

+

+\value{A \code{\link[base]{logical}}, \code{\link[base:logical]{TRUE}} if the graph is a NCI graph, \code{\link[base:logical]{FALSE}} otherwise.}

+

+\author{Laurent Jacob, Pierre Neuvial and Sandrine Dudoit}

+