CalcSilhInfo {ILoReg} | R Documentation

## Estimating optimal K using silhouette

### 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)

[Package ILoReg version 1.0.0 Index]