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Bioconductor - skewr

skewr

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

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

Bioconductor version: Release (3.21)

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 "4.5") 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 1.40.0 In Bioconductor since BioC 3.1 (R-3.2) (10 years) License GPL-2 Depends R (>= 3.1.1), methylumi, wateRmelon, mixsmsn, IlluminaHumanMethylation450kmanifest Imports minfi, S4Vectors(>= 0.19.1), RColorBrewer System Requirements URL See More Package Archives

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


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