methylumi

DOI: 10.18129/B9.bioc.methylumi    

This package is for version 3.8 of Bioconductor; for the stable, up-to-date release version, see methylumi.

Handle Illumina methylation data

Bioconductor version: 3.8

This package provides classes for holding and manipulating Illumina methylation data. Based on eSet, it can contain MIAME information, sample information, feature information, and multiple matrices of data. An "intelligent" import function, methylumiR can read the Illumina text files and create a MethyLumiSet. methylumIDAT can directly read raw IDAT files from HumanMethylation27 and HumanMethylation450 microarrays. Normalization, background correction, and quality control features for GoldenGate, Infinium, and Infinium HD arrays are also included.

Author: Sean Davis, Pan Du, Sven Bilke, Tim Triche, Jr., Moiz Bootwalla

Maintainer: Sean Davis <sdavis2 at mail.nih.gov>

Installation

To install this package, start R (version "3.5") and enter:

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")
BiocManager::install("methylumi")

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

Documentation

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

browseVignettes("methylumi")

 

PDF	R Script	An Introduction to the methylumi package
PDF	R Script	Working with Illumina 450k Arrays using methylumi
PDF		Reference Manual
Text		README

Details

biocViews	CpGIsland, DNAMethylation, Preprocessing, QualityControl, Software, TwoChannel
Version	2.28.0
In Bioconductor since	BioC 2.5 (R-2.10) (9.5 years)
License	GPL-2
Depends	Biobase, methods, R (>= 2.13), scales, reshape2, ggplot2, matrixStats, FDb.InfiniumMethylation.hg19(>= 2.2.0), minfi
Imports	BiocGenerics, S4Vectors, IRanges, GenomeInfoDb, GenomicRanges, SummarizedExperiment, Biobase, graphics, lattice, annotate, genefilter, AnnotationDbi, minfi, stats4, illuminaio
LinkingTo
Suggests	lumi, lattice, limma, xtable, SQN, MASS, matrixStats, parallel, rtracklayer, Biostrings, methyAnalysis, TCGAMethylation450k, IlluminaHumanMethylation450kanno.ilmn12.hg19, FDb.InfiniumMethylation.hg18(>= 2.2.0), Homo.sapiens, knitr
SystemRequirements
Enhances
URL
BugReports	https://github.com/seandavi/methylumi/issues/new
Depends On Me	bigmelon, RnBeads, skewr, wateRmelon
Imports Me	ffpe, lumi, methyAnalysis, missMethyl
Suggests Me
Links To Me
Build Report

Package Archives

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

Source Package	methylumi_2.28.0.tar.gz
Windows Binary	methylumi_2.28.0.zip
Mac OS X 10.11 (El Capitan)	methylumi_2.28.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/methylumi
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/methylumi
Package Short Url	http://bioconductor.org/packages/methylumi/
Package Downloads Report	Download Stats