1. DEsubs
  2. Commit 2b1cc5a12466f070fab116cb4e7efd25b3abdcd0
Browse code

Compatibility corrections

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/DEsubs@128206 bc3139a8-67e5-0310-9ffc-ced21a209358

Panos Balomenos authored on 06/04/2017 22:53:15
Showing 4 changed files
DESCRIPTION
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@@ -1,5 +1,5 @@
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 Package: DEsubs
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-Version: 1.1.2
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+Version: 1.1.3
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 Date: 2015-07-19
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 Title: DEsubs: an R package for flexible identification of
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         differentially expressed subpathways using RNA-seq expression
inst/NEWS
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@@ -1,3 +1,5 @@
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+1.1.3:  - Minor compatibility update.
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+
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 1.1.2:  - All visualization functions now return visualized data.
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         - Added support for organism Danio rerio (zebrafish).
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man/geneVisualization.Rd
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@@ -75,7 +75,7 @@ load(system.file('extdata', 'data.RData', package='DEsubs'))
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 res <- geneVisualization(
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             DEsubs.out=DEsubs.out, top=10,
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             measures.topological=c( 'degree', 'betweenness', 'closeness',
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-                                    'hub_score', 'eccentricity', 'page_rank'),
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+                                    'eccentricity', 'page_rank'),
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             measures.functional=c(  'KEGG',
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                                     'Disease_OMIM', 'Disease_GAD',
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                                     'Drug_DrugBank','miRNA', 'TF'),
vignettes/DEsubs.Rmd
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@@ -695,7 +695,7 @@ The total picture of the enriched subpathways is performed with dot plots.
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 res <- geneVisualization(
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             DEsubs.out=DEsubs.out, top=10,
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             measures.topological=c( 'degree', 'betweenness', 'closeness',
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-                                    'hub_score', 'eccentricity', 'page_rank'),
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+                                    'eccentricity', 'page_rank'),
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             measures.functional=c(  'KEGG', 'GO_bp','GO_cc', 'GO_mf',
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                                     'Disease_OMIM', 'Disease_GAD',
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                                     'Drug_DrugBank','miRNA', 'TF'),
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@@ -751,7 +751,7 @@ res <- geneVisualization(
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             DEsubs.out=DEsubs.out,
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             top=12,
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             measures.topological=c( 'degree', 'betweenness', 'closeness',
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-                                    'hub_score', 'eccentricity', 'page_rank'),
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+                                    'eccentricity', 'page_rank'),
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             measures.functional=NULL,
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             measures.barplot=FALSE,
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             size.topological=c(5,4),