get_stats-ConsensusPartition-method: Get statistics

In jokergoo/cola: A Framework for Consensus Partitioning

Get statistics

Description

Get statistics

Usage

## S4 method for signature 'ConsensusPartition'
get_stats(object, k = object@k, all_stats = FALSE)

Arguments

object	A ConsensusPartition-class object.
k	Number of subgroups. The value can be a vector.
all_stats	Whether to show all statistics that were calculated. Used internally.

Details

The statistics are:

1-PAC

1 - proportion of ambiguous clustering, calculated by PAC.

mean_silhouette

The mean silhouette score. See https://en.wikipedia.org/wiki/Silhouette_(clustering) .

concordance

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

area_increased

The increased area under eCDF (the empirical cumulative distribution function) curve to the previous k.

Rand

This 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 .

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.

Author(s)

Zuguang Gu <[e-mail]>

Examples

data(golub_cola)
obj = golub_cola["ATC", "skmeans"]
get_stats(obj)
get_stats(obj, k = 2)

jokergoo/cola documentation built on Feb. 29, 2024, 1:41 a.m.