TCGAanalyze_Clustering {TCGAbiolinks} | R Documentation

## Hierarchical cluster analysis

### Description

Hierarchical cluster analysis using several methods such as ward.D", "ward.D2", "single", "complete", "average" (= UPGMA), "mcquitty" (= WPGMA), "median" (= WPGMC) or "centroid" (= UPGMC).

### Usage

    TCGAanalyze_Clustering(tabDF, method, methodHC = "ward.D2")

### Arguments

`tabDF` | is a dataframe or numeric matrix, each row represents a gene, each column represents a sample come from TCGAPrepare.
`method` | is method to be used for generic cluster such as 'hclust' or 'consensus'
`methodHC` | is method to be used for Hierarchical cluster.

### Value

object of class hclust if method selected is 'hclust'. If method selected is 'Consensus' returns a list of length maxK (maximum cluster number to evaluate.). Each element is a list containing consensusMatrix (numerical matrix), consensusTree (hclust), consensusClass (consensus class asssignments). ConsensusClusterPlus also produces images.

[Package TCGAbiolinks version 2.8.4 Index]