plotCtrl {ENmix}R Documentation

Internal control plot

Description

The function will generate a series of internal control plots, which are similar to the plots from Illumina genomic studio software. Users should refer to the software's 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 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)
}}

[Package ENmix version 1.25.1 Index]