biosigner (version 1.0.4)

getSignatureLs: Signatures selected by the models

Description

List of 'S' (or 'S' and 'A') signatures for each classifier

Usage

## S3 method for class 'biosign':
getSignatureLs(object, tierC = c("S", "AS")[1])

Arguments

object

An S4 object of class biosign, created by the biosign function.

tierC

Character: defines whether signatures from the 'S' tier only (default) or the ('S' and 'A') tiers should be returned

Value

• List of 'S' (or 'S' and 'A') signatures for each classifier

Examples

## loading the diaplasma dataset

data(diaplasma)
attach(diaplasma)

## restricting to a smaller dataset for this example

featureSelVl <- variableMetadata[, "mzmed"] >= 490 & variableMetadata[, "mzmed"] < 500
dataMatrix <- dataMatrix[, featureSelVl]
variableMetadata <- variableMetadata[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(dataMatrix, sampleMetadata[, "type"], bootI = 5)

## individual boxplot of the selected signatures

getSignatureLs(diaSign)

detach(diaplasma)