funtooNorm

DOI: 10.18129/B9.bioc.funtooNorm    

This package is for version 3.9 of Bioconductor; for the stable, up-to-date release version, see funtooNorm.

Normalization Procedure for Infinium HumanMethylation450 BeadChip Kit

Bioconductor version: 3.9

Provides a function to normalize Illumina Infinium Human Methylation 450 BeadChip (Illumina 450K), correcting for tissue and/or cell type.

Author: Celia Greenwood <celia.greenwood at mcgill.ca>,Stepan Grinek <stepan.grinek at ladydavis.ca>, Maxime Turgeon <maxime.turgeon at mail.mcgill.ca>, Kathleen Klein <kathleen.klein at mail.mcgill.ca>

Maintainer: Kathleen Klein <kathleen.klein at mail.mcgill.ca>

Installation

To install this package, start R (version "3.6") and enter:

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

BiocManager::install("funtooNorm")

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("funtooNorm")

 

PDF	R Script	Normalizing Illumina Infinium Human Methylation 450k for multiple cell types with funtooNorm
PDF		Reference Manual
Text		NEWS

Details

biocViews	DNAMethylation, Normalization, Preprocessing, Software
Version	1.8.0
In Bioconductor since	BioC 3.5 (R-3.4) (2.5 years)
License	GPL-3
Depends	R (>= 3.4)
Imports	pls, matrixStats, minfi, methods, IlluminaHumanMethylation450kmanifest, IlluminaHumanMethylation450kanno.ilmn12.hg19, GenomeInfoDb, grDevices, graphics, stats
LinkingTo
Suggests	prettydoc, minfiData, knitr, rmarkdown
SystemRequirements
Enhances
URL
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report

Package Archives

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

Source Package	funtooNorm_1.8.0.tar.gz
Windows Binary	funtooNorm_1.8.0.zip
Mac OS X 10.11 (El Capitan)	funtooNorm_1.8.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/funtooNorm
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/funtooNorm
Package Short Url	https://bioconductor.org/packages/funtooNorm/
Package Downloads Report	Download Stats