M3C

DOI: 10.18129/B9.bioc.M3C    

This package is for version 3.7 of Bioconductor; for the stable, up-to-date release version, see M3C.

Monte Carlo Consensus Clustering

Bioconductor version: 3.7

Genome-wide data is used to stratify patients into classes using class discovery algorithms. However, we have observed systematic bias present in current state-of-the-art methods. This arises from not considering reference distributions while selecting the number of classes (K). As a solution, we developed a consensus clustering-based algorithm with a hypothesis testing framework called Monte Carlo consensus clustering (M3C). M3C uses a multi-core enabled Monte Carlo simulation to generate null distributions along the range of K which are used to calculate p values to select its value. P values beyond the limits of the simulation are estimated using a beta distribution. M3C can quantify structural relationships between clusters and uses spectral clustering to deal with non-gaussian and imbalanced structures.

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

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("M3C")

 

HTML	R Script	M3C
PDF		Reference Manual
Text		NEWS

Details

biocViews	Clustering, GeneExpression, RNASeq, Sequencing, Software, Transcription
Version	1.2.0
License	AGPL-3
Depends	R (>= 3.4.0)
Imports	ggplot2, Matrix, doSNOW, NMF, RColorBrewer, cluster, parallel, foreach, doParallel, matrixcalc, dendextend, sigclust
LinkingTo
Suggests	knitr, rmarkdown
SystemRequirements
Enhances
URL
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report

Package Archives

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

Source Package	M3C_1.2.0.tar.gz
Windows Binary	M3C_1.2.0.zip
Mac OS X 10.11 (El Capitan)	M3C_1.2.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/M3C
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/M3C
Package Short Url	http://bioconductor.org/packages/M3C/
Package Downloads Report	Download Stats