ctrlsva {ENmix} | R Documentation

## Non-negative control surrogate variables

### Description

Surrogate variables derived from intensity data for non-negative internal control probes. These variables can be modeled in association analysis to adjust for experimental batch effects.

### Usage

    ctrlsva(rgSet,percvar=0.9,npc=1,flag=1)

### Arguments

`rgSet` | An object of class `RGChannelSet`.
`percvar` | Minimum percentage of data variations can be explained by surrogate variables, range from 0 to 1,default is 0.9
`npc` | Number of surrogate variables, default is 1
`flag` | 1: select number of surrogate variables based on argument `percvar`; 2: select number of surrogate variables based on argument `npc`

### Value

ctrlsva: a matrix of surrogate variables (columns) with row corresponding to samples

### 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)) {
    sheet <- read.metharray.sheet(file.path(find.package("minfiData"),"extdata"), pattern = "csv$")
    rgSet <- read.metharray.exp(targets = sheet,extended = TRUE)
    sva<-ctrlsva(rgSet)
    }}

[Package ENmix version 1.21.6 Index]