calculate_stability {SC3} | R Documentation

## Calculate the stability index of the obtained clusters when changing `k`

### Description

Stability index shows how stable each cluster is accross the selected range of `k`. The stability index varies between 0 and 1, where 1 means that the same cluster appears in every solution for different `k`.

### Usage

    calculate_stability(consensus, k)

### Arguments

`consensus` | consensus item of the sc3 slot of an object of 'SingleCellExperiment' class
`k` | number of clusters k

### Details

Imagine a given cluster is split into `N` clusters when `k` is changed (all possible values of `k` are provided via `ks` argument in the main `sc3` function). In each of the new clusters there are `given_cells` of the given cluster and also some `extra_cells` from other clusters. Then we define stability as follows:

\frac{1}{ks*N^2}∑_{ks}∑_{N}\frac{given\_cells}{given\_cells + extra\_cells}

Where one `N` corrects for the number of clusters and the other `N` is a penalty for splitting the cluster. `ks` corrects for the range of `k`.

### Value

a numeric vector containing a stability index of each cluster

[Package SC3 version 1.16.0 Index]