rnb.execute.sva {RnBeads} | R Documentation

## rnb.execute.sva

### Description

Conduct Surrogate Variable Analysis (SVA) on the beta values of an RnBSet for given target variables

### Usage

    rnb.execute.sva(
      rnb.set,
      cmp.cols = rnb.getOption("inference.targets.sva"),
      columns.adj = rnb.getOption("covariate.adjustment.columns"),
      assoc = TRUE,
      numSVmethod = rnb.getOption("inference.sva.num.method")
    )

### Arguments

`rnb.set` | The `RnBSet` object on which the SVA should be conducted
`cmp.cols` | a vector of sample annotation column names which will be the targets of the SVA.
`columns.adj` | Column names in the table of phenotypic information to be used for confounder adjustment.
`assoc` | a flag indicating whether association information with principal components and other sample annotation should be returned
`numSVmethod` | method to estimate the number of surrogate variables. Passed to `sva`.

### Value

An object of class `SvaResult`: basically a list containing the following elements:

`num.components`

  a vector storing the number of detected SVs for each target variable

`sva.performed`

  a vector storing whether SVA was performed on a target variable and whether more than 0 SVs were found

`targets`

  a vector storing the names of the target variables

`components`

  a list storing for each target variable a matrox containing the sample-wise SVs as rows

`assoc`

  a special object containing association information of SVs with principal components and sample annotations typically only used `rnb.section.sva`.

### 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)
    has.covariates.sva(rnb.set.example,"Sample_Group")
    has.covariates.sva(rnb.set.mod,"Sample_Group")
    has.covariates.sva(rnb.set.mod,"Treatment")

[Package RnBeads version 2.10.0 Index]