plotCtrl: Internal control plot
In ENmix: Quality control and analysis tools for Illumina DNA methylation BeadChip

Description Usage Arguments Value Author(s) References Examples

The function will generate a series of internal control plots that are similar to the plots from Illumina GenomeStudio software. Users should refer to GenomeStudio online guide to interpret these figures. These figures can be used to check data quality and experimental procedures.

1	plotCtrl(rgSet,IDorder=NULL)

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

A set of internal control figures in jpeg format.

Zongli Xu

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

if (require(minfiData)) {
#rgDataSet as input
path <- file.path(find.package("minfiData"),"extdata")
rgSet <- readidat(path = path,recursive = TRUE)
plotCtrl(rgSet)

#RGChannelSet as input
pinfo=pData(RGsetEx)
IDorder=rownames(pinfo)[order(pinfo$Slide,pinfo$Array)]
plotCtrl(RGsetEx,IDorder)
}