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Showing content from https://bioconductor.org/packages/devel/bioc/html/../../bioc/html/../../bioc/html/methylumi.html below:

Bioconductor - methylumi (development version)

methylumi

This is the development version of methylumi; for the stable release version, see methylumi.

Handle Illumina methylation data

Bioconductor version: Development (3.22)

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 "4.5") and enter:


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

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

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 2.55.0 In Bioconductor since BioC 2.5 (R-2.10) (15.5 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.

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