TCGAanalyze_Clustering: Hierarchical cluster analysis

In BioinformaticsFMRP/TCGAbiolinks: TCGAbiolinks: An R/Bioconductor package for integrative analysis with GDC data

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 assignments). ConsensusClusterPlus also produces images.

BioinformaticsFMRP/TCGAbiolinks documentation built on April 12, 2024, 2:08 a.m.