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methylumi

Handle Illumina methylation data


Bioconductor version: Release (3.18)

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 <seandavi at gmail.com>

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

Installation

To install this package, start R (version "4.3") and enter:


if (!require("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")
An Introduction to the methylumi package PDF R Script
Working with Illumina 450k Arrays using methylumi PDF R Script
Reference Manual PDF
README Text

Details

biocViews CpGIsland, DNAMethylation, Preprocessing, QualityControl, Software, TwoChannel
Version 2.48.0
In Bioconductor since BioC 2.5 (R-2.10) (14.5 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, GenomicFeatures
System Requirements
URL
Bug Reports https://github.com/seandavi/methylumi/issues/new
See More
Suggests lumi, lattice, limma, xtable, SQN, MASS, matrixStats, parallel, rtracklayer, Biostrings, TCGAMethylation450k, IlluminaHumanMethylation450kanno.ilmn12.hg19, FDb.InfiniumMethylation.hg18(>= 2.2.0), Homo.sapiens, knitr
Linking To
Enhances
Depends On Me bigmelon, RnBeads, skewr, wateRmelon
Imports Me ffpe, lumi, missMethyl
Suggests Me
Links To Me
Build Report Build Report

Package Archives

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

Source Package methylumi_2.48.0.tar.gz
Windows Binary methylumi_2.48.0.zip
macOS Binary (x86_64) methylumi_2.48.0.tgz
macOS Binary (arm64) methylumi_2.48.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/methylumi
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/methylumi
Bioc Package Browser https://code.bioconductor.org/browse/methylumi/
Package Short Url https://bioconductor.org/packages/methylumi/
Package Downloads Report Download Stats