RnBeads (version 1.4.0)

set.covariates.sva: set.covariates.sva

Description

Adds the results of Surrogate Variable Analysis (SVA) to an RnBSet

Usage

set.covariates.sva(rnb.set, sva.obj)

Arguments

rnb.set

The RnBSet object to which the results should be added

sva.obj

An object of class SvaResult as returned by rnb.execute.sva.

Value

The modified RnBSet. Note that the association information will not be stored.

Examples

library(RnBeads.hg19)
data(small.example.object)
logger.start(fname=NA)
sva.obj <- rnb.execute.sva(rnb.set.example,c("Sample_Group","Treatment"),numSVmethod="be")
sva.obj$sva.performed
sva.obj$num.components
rnb.set.mod <- set.covariates.sva(rnb.set.example, sva.obj)
has.covariates.sva(rnb.set.example,"Sample_Group")
has.covariates.sva(rnb.set.mod,"Sample_Group")