Browse code

Now loading "Rgraphviz" explicitly whenever it was previously done implicitly by "KEGGgraph".

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/DEGraph@59368 bc3139a8-67e5-0310-9ffc-ced21a209358

Pierre Neuvial authored on 17/10/2011 21:22:04
Showing 10 changed files

... ...
@@ -1,7 +1,7 @@
1 1
 Package: DEGraph
2 2
 Title: Two-sample tests on a graph
3
-Version: 1.5.0
4
-Date: 2011-03-23
3
+Version: 1.5.1
4
+Date: 2011-10-16
5 5
 Author: Laurent Jacob, Pierre Neuvial and Sandrine Dudoit
6 6
 Maintainer: Laurent Jacob <laurent.jacob@gmail.com>
7 7
 Description: DEGraph implements recent hypothesis testing methods
... ...
@@ -11,12 +11,12 @@ Description: DEGraph implements recent hypothesis testing methods
11 11
   test individual genes, then test gene sets for enrichment in
12 12
   differentially expressed genes. These recent methods take into
13 13
   account the topology of the network to yield more powerful detection
14
-  procedures. DEGraph provides methods to easily test all KEGG
14
+  procedures. DEGraph provides methods to easily test all KEGG 
15 15
   pathways for differential expression on any gene expression data set
16 16
   and tools to visualize the results.
17 17
 License: GPL-3
18 18
 LazyLoad: yes
19 19
 Imports: graph, KEGGgraph, lattice, mvtnorm, R.methodsS3, RBGL, Rgraphviz, rrcov
20
-Suggests: corpcor, fields, graph, KEGGgraph, lattice, marray, RBGL, rrcov, Rgraphviz
20
+Suggests: corpcor, fields, graph, KEGGgraph, lattice, marray, RBGL, rrcov, Rgraphviz, NCIgraph
21 21
 Depends: R (>= 2.10.0), R.utils
22 22
 biocViews: Microarray, Bioinformatics, DifferentialExpression, GraphsAndNetworks
23 23
Binary files a/data/Loi2008_DEGraphVignette.RData and b/data/Loi2008_DEGraphVignette.RData differ
... ...
@@ -1,3 +1,4 @@
1
+library("Rgraphviz")
1 2
 library("KEGGgraph")
2 3
 
3 4
 ## example of KGML files
... ...
@@ -1,3 +1,4 @@
1
+library("Rgraphviz")
1 2
 library("KEGGgraph")
2 3
 
3 4
 data("Loi2008_DEGraphVignette")
... ...
@@ -116,7 +116,7 @@ library("R.utils")
116 116
 ##library(rrcov) ## for 'T2.test'
117 117
 library(corpcor)
118 118
 library(KEGGgraph)
119
-##library(Rgraphviz)
119
+library(Rgraphviz)
120 120
 ##library(RBGL)
121 121
 library(fields) # For image.plot called in plotValuedGraph
122 122
 library(lattice)
... ...
@@ -1,5 +1,6 @@
1 1
 ## Bioconductor packages
2 2
 source("http://bioconductor.org/biocLite.R")
3
+biocLite("Rgraphviz")
3 4
 biocLite("KEGGgraph")
4 5
 biocLite("marray")
5 6
 
... ...
@@ -12,6 +13,4 @@ install.packages("fields")
12 13
 ## HB's packages
13 14
 source("http://www.braju.com/R/hbLite.R")
14 15
 hbLite("R.utils")
15
-## temporary:
16
-installPackages("http://www.braju.com/R/repos/R.oo_1.7.4.tar.gz")
17 16
 
... ...
@@ -48,6 +48,7 @@
48 48
 }
49 49
 
50 50
 \examples{
51
+library("Rgraphviz")
51 52
 library("KEGGgraph")
52 53
 
53 54
 ## example of KGML files
... ...
@@ -27,3 +27,7 @@
27 27
 
28 28
 \author{Laurent Jacob, Pierre Neuvial and Sandrine Dudoit}
29 29
 
30
+\seealso{
31
+  \code{\link{parseNCInetwork}}
32
+}
33
+
... ...
@@ -59,6 +59,7 @@
59 59
 }
60 60
 
61 61
 \examples{
62
+library("Rgraphviz")
62 63
 library("KEGGgraph")
63 64
 
64 65
 data("Loi2008_DEGraphVignette")
... ...
@@ -42,6 +42,7 @@
42 42
 }
43 43
 
44 44
 \examples{
45
+library("Rgraphviz")
45 46
 library("KEGGgraph")
46 47
 
47 48
 data("Loi2008_DEGraphVignette")