getSignature: Returns a CV signature template

In FRESA.CAD: Feature Selection Algorithms for Computer Aided Diagnosis

Returns a CV signature template

Description

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

Usage

	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 Nov. 25, 2023, 1:07 a.m.