@@ -1,7 +1,7 @@

 Package: DEGraph

 Title: Two-sample tests on a graph

-Version: 1.5.1

-Date: 2011-10-16

+Version: 1.5.2

+Date: 2011-10-18

 Author: Laurent Jacob, Pierre Neuvial and Sandrine Dudoit

 Maintainer: Laurent Jacob <laurent.jacob@gmail.com>

 Description: DEGraph implements recent hypothesis testing methods

deleted file mode 100644

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

-## 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')

-  }

@@ -1,5 +1,6 @@

 library("Rgraphviz")

 library("KEGGgraph")

+library("NCIgraph")

 data("Loi2008_DEGraphVignette")

 exprData <- exprLoi2008

@@ -1,4 +1,5 @@

 library("KEGGgraph")

+library("NCIgraph")

 library("rrcov")

 data("Loi2008_DEGraphVignette")

@@ -116,6 +116,7 @@ library("R.utils")

 ##library(rrcov) ## for 'T2.test'

 library(corpcor)

 library(KEGGgraph)

+library(NCIgraph)

 library(Rgraphviz)

 ##library(RBGL)

 library(fields) # For image.plot called in plotValuedGraph

@@ -50,6 +50,7 @@

 \examples{

 library("KEGGgraph")

+library("NCIgraph")

 library("rrcov")

 data("Loi2008_DEGraphVignette")

@@ -46,6 +46,7 @@

 \examples{

 library("KEGGgraph")

+library("NCIgraph")

 library("rrcov")

 data("Loi2008_DEGraphVignette")

@@ -50,6 +50,7 @@

 \examples{

 library("KEGGgraph")

+library("NCIgraph")

 library("rrcov")

 data("Loi2008_DEGraphVignette")

@@ -61,6 +61,7 @@

 \examples{

 library("Rgraphviz")

 library("KEGGgraph")

+library("NCIgraph")

 data("Loi2008_DEGraphVignette")

 exprData <- exprLoi2008

@@ -44,6 +44,7 @@

 \examples{

 library("Rgraphviz")

 library("KEGGgraph")

+library("NCIgraph")

 data("Loi2008_DEGraphVignette")

 exprData <- exprLoi2008