MergeClusters: Merge clusters

Description Usage Arguments Value Examples

Description

MergeClusters function enables merging clusters and naming the newly formed cluster.

Usage

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MergeClusters.SingleCellExperiment(object, clusters.to.merge, new.name)

## S4 method for signature 'SingleCellExperiment'
MergeClusters(object, clusters.to.merge = "", new.name = "")

Arguments

object

of SingleCellExperiment class

clusters.to.merge

a character or numeric vector for the names of the clusters to merge

new.name

a character for the new name of the merged cluster. If left empty, the new cluster name is formed by separating the cluster names by "_".

Value

object of SingleCellExperiment class

Examples

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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)
sce <- MergeClusters(sce,clusters.to.merge=c(1,2),new.name="merged1")

ILoReg documentation built on Nov. 8, 2020, 8:20 p.m.