cluster_cells: cluster_cells

In ddiez/scmisc: Miscellaneus Tools for the Analysis of Single Cell Data

cluster_cells

Description

cluster_cells

Usage

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

## S3 method for class '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).

ddiez/scmisc documentation built on July 21, 2024, 11:35 a.m.