calc_sc3_stability_cluster {clustree} | R Documentation |
Calculate single SC3 stability
Description
Calculate the SC3 stability index for a single cluster in a set of clusterings. The index varies from 0 to 1, where 1 suggests that a cluster is more stable across resolutions.
Usage
calc_sc3_stability_cluster(clusterings, res, cluster)
Arguments
clusterings |
numeric matrix containing clustering information, each column contains clustering at a separate resolution |
res |
resolution of the cluster to calculate stability for |
cluster |
index of the cluster to calculate stability for |
Details
This index was originally introduced in the SC3
package for clustering
single-cell RNA-seq data. Clusters are awarded increased stability if they
share the same samples as a cluster at another resolution and penalised at
higher resolutions. We use a slightly different notation to describe the
score but the results are the same:
s(c_{k, i}) =
\frac{1}{size(L) + 1}
\sum_{l \in L}
\sum_{j \in N_l}
\frac{size(c_{k, i} \cap c_{l, j})}{size(c_{l, j}) * size(N_l) ^ 2}
Where:
-
c_{x, y}
is clustery
at resolutionx
-
k
is the resolution of the cluster we want to score -
i
is the index of the cluster we want to score -
L
is the set of all resolutions exceptk
-
l
is a resolution inL
-
N_l
is the set of clusters at resolutionl
that share samples withc_{k, i}
-
j
is a cluster inN_l
Value
SC3 stability index
See Also
The documentation for the calculate_stability
function in the
SC3 package