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)#>