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Adds MineICA, SomatiCA and lpNet to the repos.

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/MineICA@73179 bc3139a8-67e5-0310-9ffc-ced21a209358

Marc Carlson authored on 05/02/2013 22:15:53
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+\name{nbOccByGeneInComp}
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+\alias{nbOccByGeneInComp}
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+\title{nbOccByGeneInComp}
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+\description{For each feature/gene, this function returns the indices of the components they contribute to. }
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+\usage{nbOccByGeneInComp(Slist, cutoff, sel)}
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+\arguments{
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+  \item{Slist}{A list whose each element contains projection values of
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+    features/genes on a component.}
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+  \item{cutoff}{A threshold to be used to define a gene as contributor}
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+  \item{sel}{A list whose each element contains projection values of
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+    contributing features/genes on a component (the difference with arg
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+   \code{Slist} is that \code{sel} is already restricted to the contributing genes).}
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+}
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+
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+\value{This function returns a list which gives for each feature/gene the indices of the components it contributes to.}
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+
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+\examples{
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+ c1 <- rnorm(100); names(c1) <- paste("g",100:199,sep="")
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+ c2 <- rnorm(100); names(c2) <- paste("g",1:99,sep="")
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+ MineICA:::nbOccByGeneInComp(Slist=list(c1,c2), cutoff= 0.5)
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+
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+ }
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+\author{Anne Biton}
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+
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+