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

 Package: DEGraph

 Title: Two-sample tests on a graph

-Version: 1.9.3

+Version: 1.9.4

 Date: 2012-04-27

 Author: Laurent Jacob, Pierre Neuvial and Sandrine Dudoit

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

@@ -115,8 +115,10 @@ getKEGGPathways <- function(path=NULL, rootPath="networkData/ftp.genome.jp/pub/k

     pw <- parseKGML(pathname)

     pwInfo <- getPathwayInfo(pw)

     gr <- KEGGpathway2Graph(pw, genesOnly=TRUE, expandGenes=TRUE)

-    attr(gr, "info") <- pwInfo

-    attr(gr, "label") <- getTitle(pwInfo)

+    #attr(gr, "info") <- pwInfo

+    gr@graphData$info <- pwInfo

+    #attr(gr, "label") <- getTitle(pwInfo)

+    gr@graphData$label <- getTitle(pwInfo)

     increase(pb)

     gr

   })

@@ -196,7 +196,10 @@ getSignedGraph <- function(graph, positiveInteractionLabels=c("activation", "exp

     }

   }

-  attr(graph, 'signMat') <- signMat

+  

+  graph@graphData$signMat <- signMat

+  

+  #attr(graph, 'signMat') <- signMat

   verbose && exit(verbose)

   graph

@@ -137,7 +137,8 @@ testOneConnectedComponent <- function(graph, data, classes, ..., prop=0.2, verbo

   X2 <- t(data[, classes==cls[2]])

   ## get sign information (if any) and infer from its presence the type of graph

-  signMat <- attr(graph, 'signMat')

+  #signMat <- attr(graph, 'signMat')

+  signMat <- graph@graphData$signMat

   if (is.null(signMat)) {

     verbose && cat(verbose, "Unsigned graph")

     ## use adjacency matrix of the corresponding undirected graph