skewr

This is the development version of skewr; for the stable release version, see skewr.

All versions

3.24 (devel), 3.23 (release), 3.22, 3.21, 3.20, 3.19, 3.18, 3.17, 3.16, 3.15, 3.14, 3.13, 3.12, 3.11, 3.10, 3.9, 3.8, 3.7, 3.6, 3.5, 3.4, 3.3, 3.2, 3.1

Visualize Intensities Produced by Illumina's Human Methylation 450k BeadChip

Bioconductor version: Development (3.24)

The skewr package is a tool for visualizing the output of the Illumina Human Methylation 450k BeadChip to aid in quality control. It creates a panel of nine plots. Six of the plots represent the density of either the methylated intensity or the unmethylated intensity given by one of three subsets of the 485,577 total probes. These subsets include Type I-red, Type I-green, and Type II.The remaining three distributions give the density of the Beta-values for these same three subsets. Each of the nine plots optionally displays the distributions of the "rs" SNP probes and the probes associated with imprinted genes as series of 'tick' marks located above the x-axis.

Author: Ryan Putney [cre, aut], Steven Eschrich [aut], Anders Berglund [aut]

Maintainer: Ryan Putney <ryanputney at gmail.com>

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

Ryan Putney, Steven Eschrich, Anders Berglund. skewr: Visualize Intensities Produced by Illumina's Human Methylation 450k BeadChip. doi:10.18129/B9.bioc.skewr, R package version 1.45.0, https://bioconductor.org/packages/skewr.

Generated from the package metadata; it may differ from the package's own citation.

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("skewr")

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("skewr")

An Introduction to the skewr Package	PDF	R Script
Reference Manual	PDF

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	DNAMethylation, Preprocessing, QualityControl, Software, TwoChannel
Version	1.45.0
In Bioconductor since	BioC 3.1 (R-3.2) (11.5 years)
License	GPL-2
Depends	R (>= 3.1.1), methylumi, wateRmelon, mixsmsn, IlluminaHumanMethylation450kmanifest
Imports	minfi, S4Vectors (>= 0.19.1), RColorBrewer
System Requirements
URL

Suggests	GEOquery, knitr, minfiData
Linking To
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Depends On Me
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Build Report	Build Report, r-universe

Package Archives

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

Source Package	skewr_1.45.0.tar.gz
Windows Binary (x86_64)	skewr_1.45.0.zip
macOS Binary (big-sur-x86_64)	skewr_1.45.0.tgz
macOS Binary (sonoma-arm64)	skewr_1.45.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/skewr
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/skewr
Package Short Url	https://bioconductor.org/packages/skewr/
Package Downloads Report	Download Stats