skewr

DOI: 10.18129/B9.bioc.skewr    

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

Bioconductor version: Release (3.15)

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>

Installation

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

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

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")

 

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

Details

biocViews	DNAMethylation, Preprocessing, QualityControl, Software, TwoChannel
Version	1.28.0
In Bioconductor since	BioC 3.1 (R-3.2) (7.5 years)
License	GPL-2
Depends	R (>= 3.1.1), methylumi, wateRmelon, mixsmsn, IlluminaHumanMethylation450kmanifest
Imports	minfi, S4Vectors(>= 0.19.1), RColorBrewer
LinkingTo
Suggests	GEOquery, knitr, minfiData
SystemRequirements
Enhances
URL
Depends On Me
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Build Report

Package Archives

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

Source Package	skewr_1.28.0.tar.gz
Windows Binary	skewr_1.28.0.zip (64-bit only)
macOS Binary (x86_64)	skewr_1.28.0.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