getEset: getEset method

In ropls: PCA, PLS(-DA) and OPLS(-DA) for multivariate analysis and feature selection of omics data

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, [e-mail]

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)

ropls documentation built on Nov. 8, 2020, 7:46 p.m.