cluster_sce: Perform clustering on a SingleCellExperiment object

In AlexsLemonade/scpcaTools: Single cell data tools for ScPCA

Perform clustering on a SingleCellExperiment object

Description

Perform clustering on a SingleCellExperiment object

Usage

cluster_sce(
  sce,
  pc_name = "PCA",
  BLUSPARAM,
  cluster_column_name,
  seed = NULL,
  ...
)

Arguments

sce	SingleCellExperiment object that requires clustering
pc_name	The name used to access the PCA results stored in the SingleCellExperiment object; default is "PCA"
BLUSPARAM	A BlusterParam object specifying the clustering algorithm to use and any additional clustering options
cluster_column_name	The name of the column to store the clustering results in the SCE; for naming you may want to include the type of clustering and k value of centers, e.g. 'kmeans_10'
seed	Seed for reproducibility of clustering results
...	Additional arguments to provide to 'bluster::clusterRows()'

Value

SingleCellExperiment object containing clustering results

Examples

 ## Not run: 
  # Perform K-means clustering with 10 centers
  cluster_sce(sce, "PCA", bluster::KmeansParam(centers = 10), "kmeans_10")
 
## End(Not run)

AlexsLemonade/scpcaTools documentation built on July 12, 2024, 8:34 a.m.