MergeClusters: Merge clusters

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

Merge clusters

Description

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

Usage

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

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")

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