calculate_stability: Calculate the stability index of the obtained clusters when...
In brickyyyy/SC3min: Minimized Single-Cell Consensus Clustering
Description
Usage
Arguments
Details
Value
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
1
Arguments
consensus
consensus item of the sc3min 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 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.
Value
a numeric vector containing a stability index of each cluster
brickyyyy/SC3min documentation built on May 8, 2019, 8:07 a.m.
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Description Usage Arguments Details Value
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
1 |
Arguments
consensus |
consensus item of the sc3min 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 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.
Value
a numeric vector containing a stability index of each cluster
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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