CalcSilhInfo: Estimating optimal K using silhouette

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

Description

The function estimates the optimal number of clusters K from the dendrogram of the hierarhical clustering using the silhouette method.

Usage

CalcSilhInfo.SingleCellExperiment(object, K.start, K.end)

## S4 method for signature 'SingleCellExperiment'
CalcSilhInfo(object, K.start = 2, K.end = 50)

Arguments

object	of SingleCellExperiment class
K.start	a numeric for the smallest K value to be tested. Default is 2.
K.end	a numeric for the largest K value to be tested. Default is 50.

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 <- CalcSilhInfo(sce)

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