biosigner (version 1.0.6)

biosign-class: Class "biosign"

Description

The biosigner object class

Objects from the Class

Objects can be created by calls of the form new("biosign", ...) or by calling the biosign function

Slots

methodVc:

character vector: selected classifier(s) ('plsda', 'randomforest', or 'svm')

accuracyMN:

numeric matrix: balanced accuracies for the full models, and the models restricted to the 'S' and 'AS' signatures

tierMC:

character matrix: contains the tier ('S', 'A', 'B', 'C', 'D', or 'E') of each feature for each classifier

yFc:

factor with two levels: response factor

modelLs:

list: selected classifier(s) trained on the subset restricted to the 'S' features

signatureLs:

list: 'S' signatures for each classifier

xSubMN:

matrix: dataset restricted to the 'S' tier

AS:

list: 'AS' signatures and corresponding trained classifiers, in addition to the dataset restricted to tiers 'S' and 'A' ('xMN') and the labels ('yFc')

Methods

plot

signature(object = "biosign"): plots the tiers or the boxplots of the biomarkers selected by all the classifiers

predict

signature(object = "biosign"): predicts values based upon the classifiers trained on the 'S' signature

See Also

biosign,

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)

detach(diaplasma)