missMethyl

This package is for version 3.6 of Bioconductor; for the stable, up-to-date release version, see missMethyl.

Analysing Illumina HumanMethylation BeadChip Data

Bioconductor version: 3.6

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 (version "3.4") and enter:


if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("missMethyl")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation


Reference Manual	PDF
NEWS	Text

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	DNAMethylation, DifferentialMethylation, GeneSetEnrichment, GeneticVariability, GenomicVariation, MethylationArray, Normalization, Software
Version	1.12.0
In Bioconductor since	BioC 3.0 (R-3.1) (9.5 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, GO.db, IlluminaHumanMethylationEPICmanifest, IlluminaHumanMethylationEPICanno.ilm10b2.hg19
System Requirements
URL

Suggests	minfiData, BiocStyle, knitr, rmarkdown, edgeR, tweeDEseqCountData
Linking To
Enhances
Depends On Me
Imports Me	ChAMP, DMRcate, MEAL
Suggests Me	RnBeads
Links To Me
Build Report	Build Report

Package Archives

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

Source Package	missMethyl_1.12.0.tar.gz
Windows Binary	missMethyl_1.12.0.zip
Mac OS X 10.11 (El Capitan)	missMethyl_1.12.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/missMethyl
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/missMethyl
Package Short Url	https://bioconductor.org/packages/missMethyl/
Package Downloads Report	Download Stats
Old Source Packages for BioC 3.6	Source Archive