ctrlsva: Non-negative internal control surrogate variables

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

Non-negative internal control surrogate variables

Description

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

Usage

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

Arguments

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

Value

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.

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

xuz1/ENmix documentation built on Aug. 5, 2023, 7:11 a.m.