@@ -1,12 +1,11 @@

 Package: DEsubs

-Version: 1.3.0

-Date: 2015-07-19

+Version: 1.3.1

+Date: 2017-07-23

 Title: DEsubs: an R package for flexible identification of

         differentially expressed subpathways using RNA-seq expression

         experiments

 Author: Aristidis G. Vrahatis and Panos Balomenos

-Maintainer: Aristidis G. Vrahatis <agvrahatis@upatras.gr> and Panos

-        Balomenos <balomenos@upatras.gr>

+Maintainer: Aristidis G. Vrahatis <agvrahatis@upatras.gr>, Panos Balomenos <balomenos@upatras.gr>

 Description: DEsubs is a network-based systems biology package that

         extracts disease-perturbed subpathways within a pathway network

         as recorded by RNA-seq experiments. It contains an extensive

@@ -34,7 +34,7 @@ importFrom( 'graph',

 importFrom( 'RBGL',

                 'kCliques')

 importFrom( 'igraph',

-                'as_graphnel',

+                'igraph.to.graphNEL',

                 'graph_from_edgelist',

                 'as_data_frame',

                 'closeness',

@@ -91,9 +91,11 @@ geneVisualization <- function ( DEsubs.out,

     # Analysis #3

     if (  measures.barplot )

     {

-

-        names(topGenes) <- .changeAnnotation(annData=names(topGenes), 

-                                    org='hsa', choice='entrezToHGNC')

+        if ( org == 'hsa' )

+        {

+            names(topGenes) <- .changeAnnotation(annData=names(topGenes), 

+                                        org='hsa', choice='entrezToHGNC')

+        }

         .matrixVisualization( -log10(topGenes), type='barplot', title='',

                             colors=colors.barplot, 

@@ -158,9 +160,12 @@ geneVisualization <- function ( DEsubs.out,

     if ( visualize )

     {

-        rownames(ranking) <- .changeAnnotation( annData=rownames(ranking), 

-                                                org='hsa',

-                                                choice='entrezToHGNC')

+        if (org == 'hsa')

+        {

+            rownames(ranking) <- .changeAnnotation( annData=rownames(ranking), 

+                                                    org='hsa',

+                                                    choice='entrezToHGNC')

+        }

         .matrixVisualization( dataVis=as.matrix(ranking), 

                                 type='heatmap', title='topological',

@@ -315,7 +315,8 @@ subpathwayTypes <- function(grouping='all')

             p <- gsub('-cliques', '', method)

             k <- as.numeric(gsub('component.', '', p))

-            g <- as_graphnel( gi )

+            # g <- as_graphnel( gi )

+            g <- igraph.to.graphNEL( gi )

             ksubs <- kCliques(ugraph(g))[paste0(k, '-cliques')][[1]]

             ksubs <- lapply(ksubs, function(x) { matrix(x, nrow=1) } )

@@ -1,3 +1,5 @@

+1.3.1:  - Minor compatibility update (igraph).

+

 1.1.3:  - Minor compatibility update.

 1.1.2:  - All visualization functions now return visualized data.