plotCtrl {ENmix} | R Documentation

## Plot internal controls of 450K or MethylationEPIC BeadChip.

### 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)
    }}

[Package ENmix version 1.21.6 Index]