ctrlsva {ENmix} | R Documentation |
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.
ctrlsva(rgSet,percvar=0.9,npc=1,flag=1)
rgSet |
An object of class |
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 |
ctrlsva: a matrix of surrogate variables (columns) with row corresponding to samples
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(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) }}