suggest_best_k-ConsensusPartition-method {cola}R Documentation

Suggest the best number of partitions

Description

Suggest the best number of partitions

Usage

## S4 method for signature 'ConsensusPartition'
suggest_best_k(object, jaccard_index_cutoff = 0.95)

Arguments

object

A ConsensusPartition-class object.

jaccard_index_cutoff

The cutoff for Jaccard index compared to previous k.

Details

The best k is selected according to following rules:

1. k with rand index larger than jaccard_index_cutoff are removed. If all k are removed, the best k is defined as NA. 2. If there are some k having 1-PAC larger than 0.9, the largest k is selected as the best k. 3. If it does not fit rule 2, the k with highest vote of highest 1-PAC, mean_silhouette and concordance scores is selected as the best k.

suggest_best_k function only gives suggestion of selecting a reasonable best k. Users still need to look at the plots (e.g. by select_partition_number or consensus_heatmap functions), or even by checking whether the subgrouping gives a reasonable signatures by get_signatures, to pick a reasonable k that best explains their study.

The best k with 1-PAC larger than 0.9 is treated as a stable partition.

Value

The best k.

Author(s)

Zuguang Gu <z.gu@dkfz.de>

Examples

data(cola_rl)
obj = cola_rl["sd", "kmeans"]
suggest_best_k(obj)

[Package cola version 1.0.1 Index]