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 2.12.2 Index]