Description Usage Arguments Details Value

View source: R/ShinyFunctions.R

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 sc3 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 `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`

.

a numeric vector containing a stability index of each cluster

hemberg-lab/SC3 documentation built on May 11, 2018, 4:32 p.m.

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