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{selectContrib}
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+\alias{selectContrib}
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+\alias{selectContrib,IcaSet-method}
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+\alias{selectContrib,IcaSet,numeric,character-method}
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+\alias{selectContrib,list,numeric,ANY}
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+\alias{selectContrib,list,numeric,ANY-method}
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+ |
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+ |
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+\title{Select contributing features/genes}
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+\usage{
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+ selectContrib(object, cutoff, level, ...) |
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+} |
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+\arguments{
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+ \item{object}{Either an \code{IcaSet} object, or a list
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+ of projection vectors, e.g the list of feature or gene |
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+ projections on each component.} |
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+ |
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+ \item{cutoff}{The threshold according to which the
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+ elements will be selected. Must be either of length 1 and the same treshold is |
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+ applied to all components, or of length equal to the number of |
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+ components in order to use a specific threshold for each component.} |
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+ |
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+ \item{level}{The level of the selection: either \code{"genes"} to select
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+ contributing genes using \code{SByGene(icaSet)}, or \code{"features"}
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+ to select contributing features using \code{S(icaSet)}. }
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+ \item{...}{...}
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+} |
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+\value{
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+ A list of projections restricted to the elements that are |
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+ higher than \code{cutoff}.
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+} |
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+\description{
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+ This function selects elements whose absolute scaled |
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+ values exceed a given threshold. |
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+} |
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+\details{
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+ Each vector is first scaled and then only elements with |
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+ an absolute scaled value higher than \code{cutoff} are
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+ kept. |
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+} |
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+\examples{
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+\dontrun{
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+## load an example of icaSet |
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+data(icaSetCarbayo) |
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+ |
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+##### ========= |
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+#### When arg 'object' is an IcaSet object |
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+##### ========= |
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+ |
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+## select contributing genes |
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+selectContrib(object=icaSetCarbayo, cutoff=3, level="genes") |
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+ |
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+## select contributing features |
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+selectContrib(object=icaSetCarbayo, cutoff=3, level="features") |
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+ |
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+##### ========= |
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+#### When arg 'object' is a list |
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+##### ========= |
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+ c1 <- rnorm(100); names(c1) <- 100:199 |
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+ c2 <- rnorm(100); names(c2) <- 1:99 |
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+ selectContrib(object=list(c1,c2), cutoff= 0.5) |
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+ |
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+## select contributing features |
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+contribFlist <- selectContrib(Slist(icaSetCarbayo), 3) |
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+ |
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+## select contributing genes |
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+contribGlist <- selectContrib(SlistByGene(icaSetCarbayo), 3) |
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+ |
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+ |
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+} |
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+} |
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+\author{
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+ Anne Biton |
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+} |
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+ |