M3C
This package is for version 3.6 of Bioconductor; for the stable, up-to-date release version, see M3C.
Monte Carlo Consensus Clustering
Bioconductor version: 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>
citation("M3C")):
Installation
To install this package, start R (version "3.4") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("M3C")
For older versions of R, please refer to the appropriate Bioconductor release.
Documentation
| Reference Manual | |
| NEWS | Text |
Details
| biocViews | Clustering, GeneExpression, RNASeq, Sequencing, Software, Transcription |
| Version | 1.0.0 |
| In Bioconductor since | BioC 3.6 (R-3.4) (6.5 years) |
| License | AGPL-3 |
| Depends | R (>= 3.4.0) |
| Imports | ggplot2, Matrix, doSNOW, NMF, RColorBrewer, cluster, parallel, foreach, doParallel, matrixcalc |
| System Requirements | |
| URL |
See More
| Suggests | knitr, rmarkdown |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | 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 |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/M3C |
| Package Short Url | https://bioconductor.org/packages/M3C/ |
| Package Downloads Report | Download Stats |
| Old Source Packages for BioC 3.6 | Source Archive |