getEset: getEset method

In biosigner: Signature discovery from omics data

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, [e-mail]

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)

biosigner documentation built on Nov. 24, 2020, 2 a.m.