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>

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

Installation

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


if (!require("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")
Normalizing Illumina Infinium Human Methylation 450k for multiple cell types with funtooNorm PDF R Script
Reference Manual PDF
NEWS Text

Details

biocViews DNAMethylation, Normalization, Preprocessing, Software
Version 1.8.0
In Bioconductor since BioC 3.5 (R-3.4) (7 years)
License GPL-3
Depends R (>= 3.4)
Imports pls, matrixStats, minfi, methods, IlluminaHumanMethylation450kmanifest, IlluminaHumanMethylation450kanno.ilmn12.hg19, GenomeInfoDb, grDevices, graphics, stats
System Requirements
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Suggests prettydoc, minfiData, knitr, rmarkdown
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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
Bioc Package Browser https://code.bioconductor.org/browse/funtooNorm/
Package Short Url https://bioconductor.org/packages/funtooNorm/
Package Downloads Report Download Stats
Old Source Packages for BioC 3.9 Source Archive