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]|
|Bioconductor views||DNAMethylation Preprocessing QualityControl TwoChannel|
|Date of publication||None|
|Maintainer||Ryan Putney <email@example.com>|
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...
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