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

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.

Install the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("skewr")
AuthorRyan Putney [cre, aut], Steven Eschrich [aut], Anders Berglund [aut]
Bioconductor views DNAMethylation Preprocessing QualityControl TwoChannel
Date of publicationNone
MaintainerRyan Putney <ryanputney@gmail.com>
LicenseGPL-2
Version1.8.0

View on Bioconductor

Files

DESCRIPTION
NAMESPACE
R
R/snFuncs.R R/snMixFuncs.R R/snPlots.R R/snUtils.R
Thumbs.db
build
build/vignette.rds
inst
inst/doc
inst/doc/skewr.R
inst/doc/skewr.Rnw
inst/doc/skewr.pdf
man
man/getBarcodes.Rd man/getMethyLumiSet.Rd man/getSNparams.Rd man/panelPlots.Rd man/preprocess.Rd man/subsetProbes.Rd
vignettes
vignettes/skewr.Rnw
vignettes/skewr.bib
vignettes/unsrturl.bst

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

Please suggest features or report bugs with the GitHub issue tracker.

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