ctrlsva: Non-negative control surrogate variables

In xuz1/ENmix: Data preprocessing and quality control for Illumina HumanMethylation450 and MethylationEPIC BeadChip

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)
}}

xuz1/ENmix documentation built on Nov. 19, 2024, 12:12 p.m.