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
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@@ -19,7 +19,9 @@
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 \seealso{\code{\link{clipper}}}
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 \examples{
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-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)
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+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",
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+"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)
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+
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 row.names(toyEx) <- c("1;5","1;3")
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 toyEx
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 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
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-\name{prunePaths.R}
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+\name{prunePaths}
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 \alias{prunePaths}
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 \title{Summarize the paths obtained by clipper according to their similarity.}
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 \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
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new file mode 100644
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+\name{prunePaths.R}
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+\alias{prunePaths}
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+\title{Summarize the paths obtained by clipper according to their similarity.}
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+\description{This function allows the user to chose only one
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+  representant of those paths that have more than 1-thr similarity. The
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+  best scoring path is choosen.}
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+\usage{prunePaths(pathSummary, thr=NULL, clust=NULL, sep=";")}
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+\arguments{
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+  \item{pathSummary}{a matrix resulting from clipper function.}
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+  \item{thr}{a dissimilarity threshold. NULL means no pruning.}
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+  \item{clust}{filename where path-cluster is saved. NULL means no
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+    cluster saved.}
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+  \item{sep}{the separator to split genes for similarity
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+    computation. Default = ;}
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+}
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+
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+\value{a matrix}
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+
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+\seealso{\code{\link{clipper}}}
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+
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+\examples{
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+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)
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+row.names(toyEx) <- c("1;5","1;3")
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+toyEx
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+prunePaths(toyEx, thr=0.1)
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+}
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\ No newline at end of file