TCGAanalyze_Clustering: Hierarchical cluster analysis

Description Usage Arguments Value

View source: R/analyze.R

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

1
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.


TCGAbiolinks documentation built on Nov. 8, 2020, 5:37 p.m.