plotCtrl: Internal control plot

In xuz1/ENmix: Quality control and analysis tools for Illumina DNA methylation BeadChip

Internal control plot

Description

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.

Usage

plotCtrl(rgSet,IDorder=NULL)

Arguments

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.

Value

A set of internal control figures in jpeg format.

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 (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)
}

xuz1/ENmix documentation built on Nov. 24, 2024, 4:31 a.m.