getSignatureLs: Signatures selected by the models

In biosigner: Signature discovery from omics data

Description

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

Usage

getSignatureLs(object, tierC = c("S", "AS")[1], ...)

## S4 method for signature '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
...	Currently not used.

Value

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

Author(s)

Philippe Rinaudo and Etienne Thevenot (CEA)

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)

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