DaMiR.SVadjust {DaMiRseq} | R Documentation

## Remove variable effects from expression data

### Description

This function removes surrogate or other confounding variable effects from normalized expression data by the usage of `removeBatchEffect` function of `limma` package.

### Usage

    DaMiR.SVadjust(data, sv, n.sv)

### Arguments

`data` | A SummarizedExpression object
`sv` | The matrix of surrogate variables identified by `DaMiR.SV` function
`n.sv` | The number of surrogate variables to be used to adjust the data

### Value

A SummarizedExpression object containing a matrix of log-expression values with sv effects removed and the data frame of the variables.

### Author(s)

Mattia Chiesa, Luca Piacentini

### See Also

`removeBatchEffect`, `DaMiR.SV`

### Examples

    # use example data:
    data(data_norm)
    data(sv)
    data_adjust <- DaMiR.SVadjust(data_norm, sv = sv, n.sv = 3)

[Package DaMiRseq version 2.0.0 Index]