cluster_cells

cluster_cells

cluster_cells(x, method = "kmeans", ...)

# S3 method for SingleCellExperiment
cluster_cells(
  x,
  method = "kmeans",
  ncluster = NULL,
  assay.name = "logcounts",
  coord.name = "PCA",
  column.name = "cluster",
  hclust.method = "ward.D",
  dist.method = "euclidean",
  resolution = 1,
  algorithm = 3,
  ...
)

Arguments

x

object with data matrix.

method

type of dimensionality reduction.

...

arguments passed down to methods.

ncluster

number of clusters.

assay.name

name of assay slot.

coord.name

name of reducedDim slot.

column.name

name of column to store cluster class.

hclust.method

method for hierarchical clustering (default: ward.D).

dist.method

method for distance calculation (default: euclidean).

resolution

parameter for seurat method (see ?Seurat::FindClusters).

algorithm

parameter for seurat method (see ?Seurat::FindClusters).