runKMeans {singleCellTK} | R Documentation |
Perform KMeans clustering on a
SingleCellExperiment
object, with
kmeans
.
runKMeans( inSCE, useReducedDim = "PCA", clusterName = "KMeans_cluster", nCenters, nIter = 10, nStart = 1, seed = 12345, algorithm = c("Hartigan-Wong", "Lloyd", "MacQueen") )
inSCE |
A |
useReducedDim |
A single |
clusterName |
A single |
nCenters |
An |
nIter |
An |
nStart |
An |
seed |
An |
algorithm |
A single |
The input SingleCellExperiment
object with factor
cluster labeling updated in
colData(inSCE)[[clusterName]]
.
data("mouseBrainSubsetSCE") mouseBrainSubsetSCE <- runKMeans(mouseBrainSubsetSCE, useReducedDim = "PCA_logcounts", nCenters = 2)