R: get.covariates.sva

get.covariates.sva {RnBeads}

R Documentation

get.covariates.sva

Description

Retrieves an NxK table of Surrogate variables stored in an RnBSet for a given target variable

Usage

get.covariates.sva(rnb.set, target)

Arguments

`rnb.set`	`RnBSet` object
`target`	target variable. Must be in `pheno(rnb.set)` and belong to target variables for which the SVs have already been computed and stored in the RnBSet.

Value

an NxK table of K Surrogate variables stored for N samples of the rnb.set. NULL if the components have not been computed or added to rnb.set.

Author(s)

Fabian Mueller

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)
get.covariates.sva(rnb.set.mod,"Sample_Group")

[Package RnBeads version 2.5.0 Index]