% Generated by roxygen2: do not edit by hand

 % Please edit documentation in R/runCluster.R

 \name{runKMeans}
 \alias{runKMeans}
 \title{Get clustering with KMeans}
 \usage{
 runKMeans(
   inSCE,

   nCenters,

   useReducedDim = "PCA",
   clusterName = "KMeans_cluster",

   nComp = 10,

   nIter = 10,
   nStart = 1,
   seed = 12345,
   algorithm = c("Hartigan-Wong", "Lloyd", "MacQueen")
 )
 }
 \arguments{

 \item{inSCE}{A \linkS4class{SingleCellExperiment} object.}

 \item{nCenters}{An \code{integer}, the number of centroids (clusters).}
 

 \item{useReducedDim}{A single \code{character}, specifying which
 low-dimension representation to perform the clustering algorithm on. Default
 \code{"PCA"}.}
 
 \item{clusterName}{A single \code{character}, specifying the name to store

 the cluster label in \code{\link{colData}}. Default \code{"KMeans_cluster"}.}

 \item{nComp}{An \code{integer}. The number of components to use for K-Means.

 Default \code{10}. See Detail.}

 
 \item{nIter}{An \code{integer}, the maximum number of iterations allowed.
 Default \code{10}.}
 
 \item{nStart}{An \code{integer}, the number of random sets to choose. Default
 \code{1}.}
 
 \item{seed}{An \code{integer}. The seed for the random number generator.
 Default \code{12345}.}
 
 \item{algorithm}{A single \code{character}. Choose from
 \code{"Hartigan-Wong"}, \code{"Lloyd"}, \code{"MacQueen"}. May be
 abbreviated. Default \code{"Hartigan-Wong"}.}
 }
 \value{

 The input \linkS4class{SingleCellExperiment} object with
 \code{factor} cluster labeling updated in

 \code{colData(inSCE)[[clusterName]]}.
 }
 \description{

 Perform KMeans clustering on a

 \linkS4class{SingleCellExperiment} object, with \code{\link[stats]{kmeans}}.

 }
 \examples{
 data("mouseBrainSubsetSCE")
 mouseBrainSubsetSCE <- runKMeans(mouseBrainSubsetSCE,
                                  useReducedDim = "PCA_logcounts",
                                  nCenters = 2)
 }