Browse code

PN: Removed R/is.NCIgraph.R which is already in package NCIgraph.

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/DEGraph@59413 bc3139a8-67e5-0310-9ffc-ced21a209358

Pierre Neuvial authored on 19/10/2011 08:14:07
Showing 10 changed files

... ...
@@ -1,7 +1,7 @@
1 1
 Package: DEGraph
2 2
 Title: Two-sample tests on a graph
3
-Version: 1.5.1
4
-Date: 2011-10-16
3
+Version: 1.5.2
4
+Date: 2011-10-18
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
8 8
deleted file mode 100644
... ...
@@ -1,48 +0,0 @@
1
-## Copyright 2011 Laurent Jacob
2
-
3
-## This file is part of DEGraph.
4
-
5
-## DEGraph is free software: you can redistribute it and/or modify
6
-## it under the terms of the GNU General Public License as published by
7
-## the Free Software Foundation, either version 3 of the License, or
8
-## (at your option) any later version.
9
-
10
-## DEGraph is distributed in the hope that it will be useful,
11
-## but WITHOUT ANY WARRANTY without even the implied warranty of
12
-## MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
13
-## GNU General Public License for more details.
14
-
15
-## You should have received a copy of the GNU General Public License
16
-## along with DEGraph.  If not, see <http://www.gnu.org/licenses/>.
17
-
18
-#########################################################################/**
19
-# @RdocFunction is.NCIgraph
20
-##
21
-## @title "Assess whether a graph is a NCI graph"
22
-##
23
-##
24
-## \description{
25
-##  @get "title".
26
-## }
27
-##
28
-## @synopsis
29
-##
30
-## \arguments{
31
-##   \item{gr}{A \code{\link[=graph-class]{graph}} object.}
32
-## }
33
-##
34
-## \value{A @logical, @TRUE if the graph is a NCI graph, @FALSE otherwise.}
35
-##
36
-## @author
37
-##
38
-## \seealso{
39
-##   @see "parseNCInetwork"
40
-## }
41
-##
42
-##*/########################################################################
43
-
44
-is.NCIgraph <- function(gr)
45
-  {
46
-    ##(length(gr@nodeData@data) > 0) && (length(grep('biopax',names(gr@nodeData@data[[1]]))) > 0)
47
-    isTRUE(class(gr) == 'NCIgraph')
48
-  }
... ...
@@ -1,5 +1,6 @@
1 1
 library("Rgraphviz")
2 2
 library("KEGGgraph")
3
+library("NCIgraph")
3 4
 
4 5
 data("Loi2008_DEGraphVignette")
5 6
 exprData <- exprLoi2008
... ...
@@ -1,4 +1,5 @@
1 1
 library("KEGGgraph")
2
+library("NCIgraph")
2 3
 library("rrcov")
3 4
 
4 5
 data("Loi2008_DEGraphVignette")
... ...
@@ -116,6 +116,7 @@ library("R.utils")
116 116
 ##library(rrcov) ## for 'T2.test'
117 117
 library(corpcor)
118 118
 library(KEGGgraph)
119
+library(NCIgraph)
119 120
 library(Rgraphviz)
120 121
 ##library(RBGL)
121 122
 library(fields) # For image.plot called in plotValuedGraph
... ...
@@ -50,6 +50,7 @@
50 50
 
51 51
 \examples{
52 52
 library("KEGGgraph")
53
+library("NCIgraph")
53 54
 library("rrcov")
54 55
 
55 56
 data("Loi2008_DEGraphVignette")
... ...
@@ -46,6 +46,7 @@
46 46
 
47 47
 \examples{
48 48
 library("KEGGgraph")
49
+library("NCIgraph")
49 50
 library("rrcov")
50 51
 
51 52
 data("Loi2008_DEGraphVignette")
... ...
@@ -50,6 +50,7 @@
50 50
 
51 51
 \examples{
52 52
 library("KEGGgraph")
53
+library("NCIgraph")
53 54
 library("rrcov")
54 55
 
55 56
 data("Loi2008_DEGraphVignette")
... ...
@@ -61,6 +61,7 @@
61 61
 \examples{
62 62
 library("Rgraphviz")
63 63
 library("KEGGgraph")
64
+library("NCIgraph")
64 65
 
65 66
 data("Loi2008_DEGraphVignette")
66 67
 exprData <- exprLoi2008
... ...
@@ -44,6 +44,7 @@
44 44
 \examples{
45 45
 library("Rgraphviz")
46 46
 library("KEGGgraph")
47
+library("NCIgraph")
47 48
 
48 49
 data("Loi2008_DEGraphVignette")
49 50
 exprData <- exprLoi2008