get_stat-ConsensusPartition-method: Get statistics

Description Usage Arguments Details Value Author(s) Examples

Description

Get statistics

Usage

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## S4 method for signature 'ConsensusPartition'
get_stat(object, k = object@k)

Arguments

object

a ConsensusPartition-class object.

k

number of partitions. The value can be a vector.

Details

The statistics are:

cophcor

cophenetic correlation coefficient. It measures if hierarchical clustering is applied on the consensus matrix, how good it correlates to the consensus matrix itself.

PAC

proportion of ambiguous clustering, calculated by PAC.

mean_silhouette

the mean silhouette score.

concordance

the mean probability that each partition fits the consensus partition, calculated by concordance.

area_increased

the increased area under ecdf to the previous k

Rand

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.

Jaccard

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.

Value

A matrix of partition statistics for all k.

Author(s)

Zuguang Gu <[email protected]>

Examples

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data(cola_rl)
obj = cola_rl["sd", "kmeans"]
get_stat(obj)
get_stat(obj, k = 2)

jokergoo/cola documentation built on Nov. 13, 2018, 1:22 p.m.