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{clusterSamplesByComp}
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+\alias{clusterSamplesByComp}
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+\title{Cluster samples from an IcaSet}
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+\usage{
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+ clusterSamplesByComp(icaSet, params, |
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+ funClus = c("Mclust", "kmeans", "pam", "pamk", "hclust", "agnes"),
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+ filename, clusterOn = c("A", "S"),
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+ level = c("genes", "features"), nbClus,
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+ metric = "euclidean", method = "ward", ...) |
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+} |
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+\arguments{
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+ \item{icaSet}{An \code{IcaSet} object}
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+ |
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+ \item{params}{A \code{MineICAParams} object}
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+ |
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+ \item{funClus}{The function to be used for clustering,
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+ must be one of |
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+ \code{c("Mclust","kmeans","pam","pamk","hclust","agnes")}}
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+ |
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+ \item{filename}{A file name to write the results of the
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+ clustering in} |
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+ |
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+ \item{clusterOn}{Specifies the matrix used to apply
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+ clustering: \describe{ \item{\code{"A"}:}{the clustering
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+ is performed in one dimension, on the vector of sample |
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+ contributions,} \item{"S":}{the clustering is performed
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+ on the original data restricted to the contributing |
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+ individuals.}}} |
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+ |
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+ \item{level}{The level of projections to be used when
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+ \code{clusterOn="S"}, either \code{"features"} or
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+ \code{"genes"}.}
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+ |
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+ \item{nbClus}{The number of clusters to be computed,
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+ either a single number or a numeric vector whose length |
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+ equals the number of components. If missing (only allowed |
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+ if \code{funClus} is one of \code{c("Mclust","pamk")})}
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+ |
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+ \item{metric}{Metric used in \code{pam} and
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+ \code{hclust}, default is \code{"euclidean"}}
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+ |
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+ \item{method}{Method of hierarchical clustering, used in
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+ \code{hclust} and \code{agnes}}
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+ |
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+ \item{...}{Additional parameters required by the
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+ clustering function \code{funClus}.res <-
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+ clusterSamplesByComp(icaSet=icaSetCarbayo, params=params, |
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+ funClus="kmeans",} |
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+} |
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+\value{
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+ A list consisting of three elements |
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+ \describe{\item{clus:}{a list specifying the sample
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+ clustering for each component,}\item{resClus:}{the
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+ complete output of the clustering |
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+ function,}\item{funClus:}{the function used to perform
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+ the clustering.}}. When \code{clusterOn="S"}, if some
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+ components were not used because no contributing elements |
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+ is selected using the cutoff, the icaSet with the |
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+ corresponding component deleted is also returned. |
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+} |
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+\description{
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+ This function allows to cluster samples according to the |
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+ results of an ICA decomposition. One clustering is run |
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+ independently for each component. |
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+} |
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+\examples{
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+data(icaSetCarbayo) |
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+params <- buildMineICAParams(resPath="carbayo/", selCutoff=4) |
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+ |
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+## cluster samples according to their contributions |
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+# using Mclust without a number of clusters |
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+res <- clusterSamplesByComp(icaSet=icaSetCarbayo, params=params, funClus="Mclust", |
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+ clusterOn="A", filename="clusA") |
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+ |
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+# using kmeans |
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+res <- clusterSamplesByComp(icaSet=icaSetCarbayo, params=params, funClus="kmeans", |
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+ clusterOn="A", nbClus=2, filename="clusA") |
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+} |
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+\author{
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+ Anne Biton |
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+} |
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+\seealso{
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+ \code{Mclust}, \code{kmeans}, \code{pam}, \code{pamk},
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+ \code{hclust}, \code{agnes}, \code{cutree}
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+} |
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+ |