1. clipper
  2. man
  3. prunePaths.Rd
Browse code

Fixed compatibility issues with igraph.

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/clipper@105931 bc3139a8-67e5-0310-9ffc-ced21a209358

Paolo Martini authored on 09/07/2015 11:00:54
Showing1 changed files
man/prunePaths.Rd
History View file @3d10914
... ... 
@@ -19,7 +19,9 @@
19 19 
 \seealso{\code{\link{clipper}}}
20 20
21 21 
 \examples{
22 
-toyEx <- matrix(c(1,1,5,3,5,2,5,3,8.2,3,2,1,0.3,0.1,2,1,"1;2;3;4;5","1;2;3","1;2;3;4;5","1;2;3","1;2;3;4;5","1;2;3","1;2;3;4;5","1;2;3"),2,12)
22 
+toyEx <- matrix(c(1,1,5,3,5,2,5,3,8.2,3,2,1,0.3,0.1,2,1,"1;2;3;4;5","1;2;3",
23 
+"1;2;3;4;5","1;2;3","1;2;3;4;5","1;2;3","1;2;3;4;5","1;2;3"),2,12)
24 
+
23 25 
 row.names(toyEx) <- c("1;5","1;3")
24 26 
 toyEx
25 27 
 prunePaths(toyEx, thr=0.1)
Browse code

Documentation updates.

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/clipper@73923 bc3139a8-67e5-0310-9ffc-ced21a209358

Paolo Martini authored on 05/03/2013 14:50:22
Showing1 changed files
man/prunePaths.Rd
History View file @7f98624
... ... 
@@ -1,4 +1,4 @@
1 
-\name{prunePaths.R}
1 
+\name{prunePaths}
2 2 
 \alias{prunePaths}
3 3 
 \title{Summarize the paths obtained by clipper according to their similarity.}
4 4 
 \description{This function allows the user to chose only one
Browse code

Adds clipper, casper and PathNet.

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/clipper@72523 bc3139a8-67e5-0310-9ffc-ced21a209358

Marc Carlson authored on 15/01/2013 01:25:22
Showing1 changed files
man/prunePaths.Rd
History View file @4ceaa10
1 1 
new file mode 100644
... ... 
@@ -0,0 +1,26 @@
1 
+\name{prunePaths.R}
2 
+\alias{prunePaths}
3 
+\title{Summarize the paths obtained by clipper according to their similarity.}
4 
+\description{This function allows the user to chose only one
5 
+  representant of those paths that have more than 1-thr similarity. The
6 
+  best scoring path is choosen.}
7 
+\usage{prunePaths(pathSummary, thr=NULL, clust=NULL, sep=";")}
8 
+\arguments{
9 
+  \item{pathSummary}{a matrix resulting from clipper function.}
10 
+  \item{thr}{a dissimilarity threshold. NULL means no pruning.}
11 
+  \item{clust}{filename where path-cluster is saved. NULL means no
12 
+    cluster saved.}
13 
+  \item{sep}{the separator to split genes for similarity
14 
+    computation. Default = ;}
15 
+}
16 
+
17 
+\value{a matrix}
18 
+
19 
+\seealso{\code{\link{clipper}}}
20 
+
21 
+\examples{
22 
+toyEx <- matrix(c(1,1,5,3,5,2,5,3,8.2,3,2,1,0.3,0.1,2,1,"1;2;3;4;5","1;2;3","1;2;3;4;5","1;2;3","1;2;3;4;5","1;2;3","1;2;3;4;5","1;2;3"),2,12)
23 
+row.names(toyEx) <- c("1;5","1;3")
24 
+toyEx
25 
+prunePaths(toyEx, thr=0.1)
26 
+}
0 27 
\ No newline at end of file