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.

Author
Ryan Putney [cre, aut], Steven Eschrich [aut], Anders Berglund [aut]
Date of publication
None
Maintainer
Ryan Putney <ryanputney@gmail.com>
License
GPL-2
Version
1.6.0

View on Bioconductor

Man pages

getBarcodes
Get barcodes from idat file names
getMethyLumiSet
Read idat files and create a 'MethyLumiSet' object
getSNparams
Estimate parameters for finite mixture of Skew-Normal...
panelPlots
Plot the distributions of the probe intensities and the...
preprocess
Normalize a MethyLumiSet object using some popular choices
subsetProbes
Conveniently subset probes by type and retrieve the...

Files in this package

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