biosigner (version 1.0.6)

getSignatureLs: Signatures selected by the models

Description

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

Usage

"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)