wateRmelon

This is the released version of wateRmelon; for the devel version, see wateRmelon.

Illumina DNA methylation array normalization and metrics

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DOI: 10.18129/B9.bioc.wateRmelon

Bioconductor version: Release (3.22)

15 flavours of betas and three performance metrics, with methods for objects produced by methylumi and minfi packages.

Author: Leo C Schalkwyk [cre, aut], Tyler J Gorrie-Stone [aut], Ruth Pidsley [aut], Chloe CY Wong [aut], Nizar Touleimat [ctb], Matthieu Defrance [ctb], Andrew Teschendorff [ctb], Jovana Maksimovic [ctb], Louis Y El Khoury [ctb], Yucheng Wang [ctb], Alexandria Andrayas [ctb]

Maintainer: Leo C Schalkwyk <lschal at essex.ac.uk>

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

Installation

To install this package, start R (version "4.5") and enter:


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

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("wateRmelon")

wateRmelon User's Guide HTML R Script

Reference Manual PDF

Need some help? Ask on the Bioconductor Support site!

Details

biocViews DNAMethylation, Microarray, Preprocessing, QualityControl, Software, TwoChannel

Version 2.16.0

In Bioconductor since BioC 2.12 (R-3.0) (12.5 years)

License GPL-3

Depends R (>= 3.5.0), Biobase, limma, methods, matrixStats, methylumi, lumi, ROC, IlluminaHumanMethylation450kanno.ilmn12.hg19, illuminaio

Imports Biobase

System Requirements

URL

Suggests RPMM, IlluminaHumanMethylationEPICanno.ilm10b2.hg19, BiocStyle, knitr, rmarkdown, IlluminaHumanMethylationEPICmanifest, irlba, FlowSorted.Blood.EPIC, FlowSorted.Blood.450k, preprocessCore

Linking To

Enhances minfi

Depends On Me bigmelon, skewr

Imports Me ChAMP, MEAT

Suggests Me RnBeads

Links To Me

Build Report Build Report

Package Archives

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

Source Package wateRmelon_2.16.0.tar.gz

Windows Binary (x86_64) wateRmelon_2.16.0.zip (64-bit only)

macOS Binary (x86_64) wateRmelon_2.16.0.tgz

macOS Binary (arm64) wateRmelon_2.16.0.tgz

Source Repository git clone https://git.bioconductor.org/packages/wateRmelon

Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/wateRmelon

Bioc Package Browser https://code.bioconductor.org/browse/wateRmelon/

Package Short Url https://bioconductor.org/packages/wateRmelon/

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