getEset {ropls} | R Documentation

## getEset method

### Description

Extracts the complemented ExpressionSet when opls has been applied to an ExpressionSet

### Usage

    getEset(object, ...)

    ## S4 method for signature 'opls'
    getEset(object)

### Arguments

`object` | An S4 object of class `opls`, created by `opls` function.
`...` | Currently not used

### Value

An S4 object of class `ExpressionSet` which contains the dataMatrix (t(exprs(eset))), and the sampleMetadata (pData(eset)) and variableMetadata (fData(eset)) with the additional columns containing the scores, predictions, loadings, VIP, coefficients etc.

### Author(s)

Etienne Thevenot, etienne.thevenot@cea.fr

### Examples

    data(sacurine)
    attach(sacurine)

    sacSet <- Biobase::ExpressionSet(assayData = t(dataMatrix),
                                     phenoData = new("AnnotatedDataFrame",
                                                     data = sampleMetadata),
                                     featureData = new("AnnotatedDataFrame",
                                                       data = variableMetadata),
                                     experimentData = new("MIAME",
                                                          title = "sacurine"))

    sacPlsda <- opls(sacSet, "gender")
    sacSet <- getEset(sacPlsda)
    head(Biobase::pData(sacSet))
    head(Biobase::fData(sacSet))

    detach(sacurine)

[Package ropls version 1.18.8 Index]