normalize450K

DOI: 10.18129/B9.bioc.normalize450K  

Preprocessing of Illumina Infinium 450K data

Bioconductor version: Release (3.16)

Precise measurements are important for epigenome-wide studies investigating DNA methylation in whole blood samples, where effect sizes are expected to be small in magnitude. The 450K platform is often affected by batch effects and proper preprocessing is recommended. This package provides functions to read and normalize 450K '.idat' files. The normalization corrects for dye bias and biases related to signal intensity and methylation of probes using local regression. No adjustment for probe type bias is performed to avoid the trade-off of precision for accuracy of beta-values.

Author: Jonathan Alexander Heiss

Maintainer: Jonathan Alexander Heiss <jonathan.heiss at posteo.de>

Installation

To install this package, start R (version "4.2") and enter:

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

BiocManager::install("normalize450K")

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("normalize450K")

 

PDF	R Script	Normalization of 450K data
PDF		Reference Manual
Text		LICENSE

Details

biocViews	DNAMethylation, MethylationArray, Microarray, Normalization, Preprocessing, Software, TwoChannel
Version	1.26.0
In Bioconductor since	BioC 3.3 (R-3.3) (7 years)
License	BSD_2_clause + file LICENSE
Depends	R (>= 3.3), Biobase, illuminaio, quadprog
Imports	utils
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Package Archives

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

Source Package	normalize450K_1.26.0.tar.gz
Windows Binary	normalize450K_1.26.0.zip
macOS Binary (x86_64)	normalize450K_1.26.0.tgz
macOS Binary (arm64)	normalize450K_1.26.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/normalize450K
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/normalize450K
Bioc Package Browser	https://code.bioconductor.org/browse/normalize450K/
Package Short Url	https://bioconductor.org/packages/normalize450K/
Package Downloads Report	Download Stats