ctrlsva: Non-negative internal control surrogate variables
In ENmix: Quality control and analysis tools for Illumina DNA methylation BeadChip

Description Usage Arguments Value Author(s) References Examples

Surrogate variables derived based on intensity data for non-negative internal control probes.

1	ctrlsva(rgSet,percvar=0.95,npc=1,flag=1)

`rgSet`	An object of class `rgDataSet` or `RGChannelSet`.
`percvar`	Minimum percentage of data variations can be explained by surrogate variables, range from 0 to 1,default is 0.95
`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`

The function will return an numerical matrix with columns indicating surrogate variables and rows corresponding to samples. These variables can be used in association analysis to adjust for experimental batch effects.

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)) {
path <- file.path(find.package("minfiData"),"extdata")
rgSet <- readidat(path = path,recursive = TRUE)
sva<-ctrlsva(rgSet)
}