getSignature: Returns a CV signature template

Description Usage Arguments Details Value Author(s)

View source: R/getSignature.r

Description

This function returns the matrix template [mean,sd,IQR] that maximizes the ROC AUC between cases of controls.

Usage

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	getSignature(
	              data,
	              varlist=NULL,
	              Outcome=NULL,
	              target=c("All","Control","Case"),
	              CVFolds=3,
	              repeats=9,
	              distanceFunction=signatureDistance,
	              ...
	)

Arguments

data

A data frame whose rows contains the sampled "subject" data, and each column is a feature.

varlist

The varlist is a character vector that list all the features to be searched by the Backward elimination forward selection procedure.

Outcome

The name of the column that has the binary outcome. 1 for cases, 0 for controls

target

The target template that will be used to maximize the AUC.

CVFolds

The number of folds to be used

repeats

how many times the CV procedure will be repeated

distanceFunction

The function to be used to compute the distance between the template and each sample

...

the parameters to be passed to the distance function

Details

The function repeats full cycles of a Cross Validation (RCV) procedure. At each CV cycle the algorithm estimate the mean template and the distance between the template and the test samples. The ROC AUC is computed after the RCV is completed. A forward selection scheme. The set of features that maximize the AUC during the Forward loop is returned.

Value

controlTemplate

the control matrix with quantile probs[0.025,0.25,0.5,0.75,0.975] that maximized the AUC (template of controls subjects)

caseTamplate

the case matrix with quantile probs[0.025,0.25,0.5,0.75,0.975] that maximized the AUC (template of case subjects)

AUCevolution

The AUC value at each cycle

featureSizeEvolution

The number of features at each cycle

featureList

The final list of features

CVOutput

A data frame with four columns: ID, Outcome, Case Distances, Control Distances. Each row contains the CV test results

MaxAUC

The maximum ROC AUC

Author(s)

Jose G. Tamez-Pena


FRESA.CAD documentation built on Jan. 13, 2021, 3:39 p.m.