suggest_best_k-ConsensusPartition-method {cola}R Documentation

Suggest the best number of subgroups

Description

Suggest the best number of subgroups

Usage

## S4 method for signature 'ConsensusPartition'
suggest_best_k(object,
    jaccard_index_cutoff = select_jaccard_cutoff(ncol(object)),
    mean_silhouette_cutoff = NULL,
    stable_PAC = 0.1, help = cola_opt$help)

Arguments

object

A ConsensusPartition-class object.

jaccard_index_cutoff

The cutoff for Jaccard index for comparing to previous k.

mean_silhouette_cutoff

Cutoff for mean silhourtte scores.

stable_PAC

Cutoff for stable PAC. This argument only take effect when mean_silhouette_cutoff is set to NULL.

help

Whether to print help message.

Details

The best k is selected according to following rules:

It should be noted that it is difficult to find the best k deterministically, we encourage users to compare results for all k and determine a proper one which best explain their studies.

Value

The best k.

See

The selection of the best k can be visualized by select_partition_number.

Author(s)

Zuguang Gu <z.gu@dkfz.de>

Examples

data(golub_cola)
obj = golub_cola["ATC", "skmeans"]
suggest_best_k(obj)

[Package cola version 2.0.0 Index]