normalize450K
This is the development version of normalize450K; for the stable release version, see normalize450K.
Preprocessing of Illumina Infinium 450K data
Bioconductor version: Development (3.24)
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>
citation("normalize450K")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
## The following initializes the development version of Bioconductor
BiocManager::install(version = "devel")
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")| Normalization of 450K data | R Script | |
| Reference Manual | ||
| LICENSE | Text |
Details
| biocViews | DNAMethylation, MethylationArray, Microarray, Normalization, Preprocessing, Software, TwoChannel |
| Version | 1.41.0 |
| In Bioconductor since | BioC 3.3 (R-3.3) (10.5 years) |
| License | BSD_2_clause + file LICENSE |
| Depends | R (>= 3.3), Biobase, illuminaio, quadprog |
| Imports | utils |
| System Requirements | |
| URL |
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| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | normalize450K_1.41.0.tar.gz |
| Windows Binary (x86_64) | normalize450K_1.41.0.zip |
| macOS Binary (big-sur-x86_64) | normalize450K_1.41.0.tgz |
| macOS Binary (sonoma-arm64) | normalize450K_1.41.0.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 |