MethylMix

DOI: 10.18129/B9.bioc.MethylMix    

MethylMix: Identifying methylation driven cancer genes

Bioconductor version: Release (3.7)

MethylMix is an algorithm implemented to identify hyper and hypomethylated genes for a disease. MethylMix is based on a beta mixture model to identify methylation states and compares them with the normal DNA methylation state. MethylMix uses a novel statistic, the Differential Methylation value or DM-value defined as the difference of a methylation state with the normal methylation state. Finally, matched gene expression data is used to identify, besides differential, functional methylation states by focusing on methylation changes that effect gene expression. References: Gevaert O. MethylMix: an R package for identifying DNA methylation-driven genes. Bioinformatics (Oxford, England). 2015;31(11):1839-41. doi:10.1093/bioinformatics/btv020. Gevaert O, Tibshirani R, Plevritis SK. Pancancer analysis of DNA methylation-driven genes using MethylMix. Genome Biology. 2015;16(1):17. doi:10.1186/s13059-014-0579-8. Pierre-Louis Cedoz, Marcos Prunello, Kevin Brennan, Olivier Gevaert; MethylMix 2.0: an R package for identifying DNA methylation genes. Bioinformatics. doi:10.1093/bioinformatics/bty156.

Author: Olivier Gevaert

Maintainer: Olivier Gevaert <olivier.gevaert at gmail.com>

Citation (from within R, enter citation("MethylMix")):

Installation

To install this package, start R and enter:

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

Documentation

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

browseVignettes("MethylMix")

 

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Details

biocViews DNAMethylation, DifferentialExpression, DifferentialMethylation, GeneExpression, GeneRegulation, MethylationArray, Network, Pathways, Software, StatisticalMethod
Version 2.10.2
In Bioconductor since BioC 3.0 (R-3.1) (4 years)
License GPL-2
Depends R (>= 3.2.0)
Imports foreach, RPMM, RColorBrewer, ggplot2, RCurl, impute, data.table, limma, R.matlab, digest
LinkingTo
Suggests BiocStyle, doParallel, testthat, knitr, rmarkdown
SystemRequirements
Enhances
URL
Depends On Me
Imports Me
Suggests Me
Build Report  

Package Archives

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Source Package MethylMix_2.10.2.tar.gz
Windows Binary MethylMix_2.10.2.zip
Mac OS X 10.11 (El Capitan) MethylMix_2.10.2.tgz
Source Repository git clone https://git.bioconductor.org/packages/MethylMix
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/MethylMix
Package Short Url http://bioconductor.org/packages/MethylMix/
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Old Source Packages for BioC 3.7 Source Archive

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