To install this package, start R and enter:

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

In most cases, you don't need to download the package archive at all.

missMethyl

 

   

Analysis of methylation array data

Bioconductor version: Release (3.3)

Normalisation and testing for differential variability and differential methylation for data from Illumina's Infinium HumanMethylation450 array. The normalisation procedure is subset-quantile within-array normalisation (SWAN), which allows Infinium I and II type probes on a single array to be normalised together. The test for differential variability is based on an empirical Bayes version of Levene's test. Differential methylation testing is performed using RUV, which can adjust for systematic errors of unknown origin in high-dimensional data by using negative control probes. Gene ontology analysis is performed by taking into account the number of probes per gene on the array.

Author: Belinda Phipson and Jovana Maksimovic

Maintainer: Belinda Phipson <belinda.phipson at mcri.edu.au>, Jovana Maksimovic <jovana.maksimovic at mcri.edu.au>

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

Installation

To install this package, start R and enter:

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

Documentation

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

browseVignettes("missMethyl")

 

PDF R Script missMethyl: analysing data from Illumina's HumanMethylation450 array
PDF   Reference Manual
Text   NEWS

Details

biocViews DNAMethylation, DifferentialMethylation, GeneSetEnrichment, GeneticVariability, GenomicVariation, MethylationArray, Normalization, Software
Version 1.6.2
In Bioconductor since BioC 3.0 (R-3.1) (1.5 years)
License GPL-2
Depends R (>= 2.3.0)
Imports limma, minfi, methylumi, IlluminaHumanMethylation450kmanifest, statmod, ruv, stringr, IlluminaHumanMethylation450kanno.ilmn12.hg19, org.Hs.eg.db, AnnotationDbi, BiasedUrn
LinkingTo
Suggests minfiData, BiocStyle, knitr, edgeR, tweeDEseqCountData
SystemRequirements
Enhances
URL
Depends On Me
Imports Me
Suggests Me Harman
Build Report  

Package Archives

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

Package Source missMethyl_1.6.2.tar.gz
Windows Binary missMethyl_1.6.2.zip
Mac OS X 10.9 (Mavericks) missMethyl_1.6.2.tgz
Subversion source (username/password: readonly)
Git source https://github.com/Bioconductor-mirror/missMethyl/tree/release-3.3
Package Short Url http://bioconductor.org/packages/missMethyl/
Package Downloads Report Download Stats

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