getEset,biosign-method {biosigner} | R Documentation

## getEset method

### Description

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

### Usage

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

### Arguments

`object` | An S4 object of class `biosign`, created by `biosign` function.

### 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 computed tiers for each feature and each classifier.

### Author(s)

Etienne Thevenot, etienne.thevenot@cea.fr

### Examples

    ## loading the diaplasma dataset

    data(diaplasma)
    attach(diaplasma)

    ## building the ExpresssionSet instance

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

    ## restricting to a smaller dataset for this example

    featureSelVl <- variableMetadata[, "mzmed"] >= 490 & variableMetadata[, "mzmed"] < 500
    diaSet <- diaSet[featureSelVl, ]

    ## signature selection for all 3 classifiers
    ## a bootI = 5 number of bootstraps is used for this example
    ## we recommend to keep the default bootI = 50 value for your analyzes

    set.seed(123)
    diaSign <- biosign(diaSet, "type", bootI = 5)

    diaSet <- biosigner::getEset(diaSign)
    head(Biobase::pData(diaSet))
    head(Biobase::fData(diaSet))

    detach(diaplasma)

[Package biosigner version 1.16.0 Index]