M3C

DOI: 10.18129/B9.bioc.M3C    

Monte Carlo Consensus Clustering

Bioconductor version: Release (3.6)

A central task in genomic data analyses for stratified medicine is class discovery which is accomplished through clustering. However, an unresolved problem with current clustering algorithms is they do not test the null hypothesis and derive p values. To solve this, we developed a novel hypothesis testing framework that uses consensus clustering called Monte Carlo Consensus Clustering (M3C). M3C use a multi-core enabled Monte Carlo simulation to generate a distribution of stability scores for each number of clusters using null datasets with the same gene-gene correlation structure as the real one. These distributions are used to derive p values and a beta distribution is fitted to the data to cheaply estimate p values beyond the limits of the simulation. M3C improves accuracy, allows rejection of the null hypothesis, removes systematic bias, and uses p values to make class number decisions. We believe M3C deals with a major pitfall in current automated class discovery tools.

Author: Christopher John [aut, cre]

Maintainer: Christopher John <chris.r.john86 at gmail.com>

Installation

To install this package, start R and enter:

## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("M3C")

Documentation

HTML	R Script	M3C
PDF		Reference Manual
Text		NEWS

Details

biocViews	Clustering, GeneExpression, RNASeq, Sequencing, Software, Transcription
Version	1.0.0
License	AGPL-3
Depends	R (>= 3.4.0)
Imports	ggplot2, Matrix, doSNOW, NMF, RColorBrewer, cluster, parallel, foreach, doParallel, matrixcalc
LinkingTo
Suggests	knitr, rmarkdown
SystemRequirements
Enhances
URL
Depends On Me
Imports Me
Suggests Me
Build Report

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package	M3C_1.0.0.tar.gz
Windows Binary	M3C_1.0.0.zip
Mac OS X 10.11 (El Capitan)	M3C_1.0.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/M3C
Package Short Url	http://bioconductor.org/packages/M3C/
Package Downloads Report	Download Stats