doc fixes; update NEWS; version bump

egonw · Apr 1, 2019 · 0e71a98 · 0e71a98
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diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,7 +1,7 @@
 Package: rWikiPathways
 Type: Package
 Title: rWikiPathways - R client library for the WikiPathways API
-Version: 1.3.2
+Version: 1.3.3
 Date: 2019-04-01
 Authors@R: c(person("Egon", "Willighagen", role = c("aut","cre"),
                      email = "egon.willighagen@gmail.com",

diff --git a/NEWS b/NEWS
@@ -1,29 +1,26 @@
-CHANGES IN VERSION 1.3.2
-------------------------
-
-BUG FIXES
-
-    o Added the missing References section to one of the vignettes
-
-CHANGES IN VERSION 1.0.0
-------------------------
-
-NEW FEATURES
-
-    o Added derivative functions for both listPathways and getPathwaysByXref to allow 
-    specifying the return of simple lists of WPIDs, URLs or names.
-    o Added support for PNG from getColoredPathway
-    o Added functions for all remaining web service API methods
-    o Added a download function for archived pathway sets in various formats
-    o Added Overview and BridgeDbR vignettes
-
-SIGNIFICANT CHANGES UNDER THE HOOD
-
-    o Updated all functions to use REST calls instead of Curl
-    o Simplified function development by abstracting as dedicated wikipathwaysGET function
-    o Added tests for all new functions
-    o Added enumerated parameters in a number of places for better input validation
-
-BUG FIXES
-
-    o First official release. No bugs... yet!
+Changes in version 1.4.0
++ Bug fixes
+    - Fixed createSubnetwork -- #43 network suids i/o names
++ Doc fixes
+    - Fixed sign in subsetting function in vignette -- user issue on bioc forum
+    - Added XML to Imports
+    - Added the missing References section to one of the vignettes
+Changes in version 1.2.0
++ Bug fixes
+    - Added method to retrieve GMT files -- #3 issue
++ Doc fixes
+    - New vignette for pathway analysis
+Changes in version 1.0.0
++ New features
+    - Added derivative functions for both listPathways and getPathwaysByXref to allow specifying the return of simple lists of WPIDs, URLs or names.
+    - Added support for PNG from getColoredPathway
+    - Added functions for all remaining web service API methods
+    - Added a download function for archived pathway sets in various formats
+    - Added Overview and BridgeDbR vignettes
++ Significant changes under the hood
+    - Updated all functions to use REST calls instead of Curl
+    - Simplified function development by abstracting as dedicated wikipathwaysGET function
+    - Added tests for all new functions
+    - Added enumerated parameters in a number of places for better input validation
++Bug fixes
+    - First official release. No bugs... yet!
diff --git a/vignettes/Pathway-Analysis.Rmd b/vignettes/Pathway-Analysis.Rmd
@@ -258,7 +258,7 @@ gwp.sig.lung.expr.df = data.frame(ID=gwp.sig.lung.expr$ID,
                                  leading_edge=gwp.sig.lung.expr$leading_edge
 )
 gwp.sig.lung.expr.df[which(gwp.sig.lung.expr.df$NES>1),] #pathways enriched for upregulated lung cancer genes
-gwp.sig.lung.expr.df[which(gwp.sig.lung.expr.df$NES<1),] #pathways enriched for downregulated lung cancer genes
+gwp.sig.lung.expr.df[which(gwp.sig.lung.expr.df$NES<-1),] #pathways enriched for downregulated lung cancer genes
 ```
 
 One of the advantages of pathway analysis is that you have *pathway models* already built and ready for data overlays. We will get to that soon in the in **Visualize** section, but first, let's see what else we can learn about the pathways hits from WikiPathways.