get_stats-ConsensusPartition-method {cola} | R Documentation |
Get statistics for the consensus partition
## S4 method for signature 'ConsensusPartition' get_stats(object, k = object@k)
object |
a |
k |
number of partitions. The value can be a vector. |
The statistics are:
cophenetic correlation coefficient. It measures if hierarchical clustering is applied on the consensus matrix, how good it correlates to the consensus matrix itself.
proportion of ambiguous clustering, calculated by PAC
.
the mean silhouette score. See https://en.wikipedia.org/wiki/Silhouette_(clustering) .
the mean probability that each partition fits the consensus partition, calculated by concordance
.
the increased area under ECDF (the empirical cumulative distribution function curve) to the previous k.
the Rand index which is the percent of pairs of samples that are both in a same cluster or both are not in a same cluster in the partition of k
and k-1
. See https://en.wikipedia.org/wiki/Rand_index .
the ratio of pairs of samples are both in a same cluster in the partition of k
and k-1
and the pairs of samples are both in a same cluster in the partition k
or k-1
.
A matrix of partition statistics.
Zuguang Gu <z.gu@dkfz.de>
data(cola_rl) obj = cola_rl["sd", "kmeans"] get_stats(obj) get_stats(obj, k = 2)