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skewr

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


Bioconductor version: Release (3.19)

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")):

Installation

To install this package, start R (version "4.4") 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")
An Introduction to the skewr Package PDF R Script
Reference Manual PDF

Details

biocViews DNAMethylation, Preprocessing, QualityControl, Software, TwoChannel
Version 1.36.0
In Bioconductor since BioC 3.1 (R-3.2) (9 years)
License GPL-2
Depends R (>= 3.1.1), methylumi, wateRmelon, mixsmsn, IlluminaHumanMethylation450kmanifest
Imports minfi, S4Vectors(>= 0.19.1), RColorBrewer
System Requirements
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Suggests GEOquery, knitr, minfiData
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Package Archives

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

Source Package skewr_1.36.0.tar.gz
Windows Binary skewr_1.36.0.zip (64-bit only)
macOS Binary (x86_64) skewr_1.36.0.tgz
macOS Binary (arm64) skewr_1.36.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/skewr
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/skewr
Bioc Package Browser https://code.bioconductor.org/browse/skewr/
Package Short Url https://bioconductor.org/packages/skewr/
Package Downloads Report Download Stats