calculate_stability: Calculate the stability index of the obtained clusters when...
In brickyyyy/MinimizedSC3: Minimized Single-Cell Consensus Clustering

Description Usage Arguments Details Value

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.

1	calculate_stability(consensus, k)

`consensus`	consensus item of the sc3min slot of an object of 'SingleCellExperiment' class
`k`	number of clusters k

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 sc3min 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.

a numeric vector containing a stability index of each cluster

brickyyyy/MinimizedSC3 documentation built on May 23, 2019, 1:45 p.m.