To install this package, start R and enter:

## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("skewr")

In most cases, you don't need to download the package archive at all.

skewr

DOI: 10.18129/B9.bioc.skewr    

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

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

Bioconductor version: Development (3.6)

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 and enter:

## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("skewr")

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 1.9.0
In Bioconductor since BioC 3.1 (R-3.2) (2.5 years)
License GPL-2
Depends R (>= 3.1.1), methylumi, wateRmelon, mixsmsn, IlluminaHumanMethylation450kmanifest
Imports minfi, IRanges, RColorBrewer
LinkingTo
Suggests GEOquery, knitr, minfiData
SystemRequirements
Enhances
URL
Depends On Me
Imports Me
Suggests Me
Build Report  

Package Archives

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

Source Package skewr_1.9.0.tar.gz
Windows Binary skewr_1.9.0.zip
Mac OS X 10.11 (El Capitan) skewr_1.9.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/skewr
Package Short Url http://bioconductor.org/packages/skewr/
Package Downloads Report Download Stats

Documentation »

Bioconductor

R / CRAN packages and documentation

Support »

Please read the posting guide. Post questions about Bioconductor to one of the following locations: