SelectKClusters: Selecting K clusters from hierarchical clustering

In elolab/iloreg: ILoReg: a tool for high-resolution cell population identification from scRNA-Seq data

Selecting K clusters from hierarchical clustering

Description

Selects K clusters from the dendrogram.

Usage

SelectKClusters.SingleCellExperiment(object, K)

## S4 method for signature 'SingleCellExperiment'
SelectKClusters(object, K = NULL)

Arguments

object	of SingleCellExperiment class
K	a positive integer denoting how many clusters to select

Value

object of SingleCellExperiment class

Examples

library(SingleCellExperiment)
sce <- SingleCellExperiment(assays = list(logcounts = pbmc3k_500))
sce <- PrepareILoReg(sce)
## These settings are just to accelerate the example, use the defaults.
sce <- RunParallelICP(sce,L=2,threads=1,C=0.1,k=5,r=1)
sce <- RunPCA(sce,p=5)
sce <- HierarchicalClustering(sce)
sce <- SelectKClusters(sce,K=5)

elolab/iloreg documentation built on March 27, 2022, 4:19 a.m.