plotCtrl: Plot internal controls of 450K or MethylationEPIC BeadChip.

In USCbiostats/ENmixUSC: Data preprocessing and quality control for Illumina HumanMethylation450 and MethylationEPIC BeadChip (USC version)

Description

Intensity data are ploted for all internal control probe types on the Illumina Infinium HumanMethylation450 or MethylationEPIC BeadChip. These figures can be used to check data quality and experimental procedures.

Usage

plotCtrl(rgSet,IDorder=NULL)

Arguments

rgSet	An object of class RGChannelSet.
IDorder	A list of sample ids in the order user specified. The list can be a subset of the samples in input dataset. If an id list is provided, all plots will be produced in the order of the list. The default is NULL.

Value

A set of jpeg figures.

Author(s)

Zongli Xu

References

Zongli Xu, Liang Niu, Leping Li and Jack A. Taylor, ENmix: a novel background correction method for Illumina HumanMethylation450 BeadChip. Nucleic Acids Research 2015.

Examples

if(FALSE){
if (require(minfiData)) {
pinfo=pData(RGsetEx)
IDorder=rownames(pinfo)[order(pinfo$Slide,pinfo$Array)]
plotCtrl(RGsetEx,IDorder)
}}

USCbiostats/ENmixUSC documentation built on June 1, 2019, 3:55 a.m.