Validator: Validate the Performance of a ForeseeModel on a new...

In JRC-COMBINE/FORESEE: A Tool for the Systematic Comparison of Translational Drug Response Modeling Pipelines

Description

The Validator evaluates the performance of the model by comparing the predicted response Foreseen to the reported, true response from the TestObject's Annotation.

Usage

Validator(Foreseen, TestObject, Evaluation)

Arguments

Foreseen	Predicted drug response of the TestObject obtained by applying the ForeseeModel.
TestObject	Object that contains all data that the model is to be tested on, especially the true, measured drug response.
Evaluation	Measure for evaluating the model performance, such as ROC-Curve, AUC or p-value of ROC-Curve, Rsquared, MSE, Correlation, F-Test, etc. The option 'fpvalue' calculates the p value of an F test on a linear model between predictions and the actual annotations, The option 'mse' calculates the mean square error of a linear model between predictions and the actual annotations, The option 'pearson' calculates the pearson correlation between predictions and the actual annotations, The option 'prauc' calculates the AUC of the precision-recall curve The option 'rocauc' calculates the AUC of the ROC curve The option 'rocpvalue' calculates the t.test p value of the ROC curve AUC versus 10000 permutated annotation values, The option 'rsquared' calculates the fraction of variance explained by a linear model between predictions and actual annotations, The option 'rsquared_adjusted' calculates the fraction of variance explained by a linear model between predictions and actual annotations, corrected the p-value of F-test, The option 'spearman'. calculates the spearman correlation between predictions and the actual annotations. The function 'listInputOptions("Validator")' returns a list of the possible options. Instead of choosing one of the implemented options, a user-defined function can be used as an input.

Value

Performance

Evaluation Measure of the Predictability of the ForeseeModel trained on the TrainObject and tested on the TestObject.

Examples

Validator(rep(1,length(GSE6434$Annotation)),GSE6434,"rocauc")

JRC-COMBINE/FORESEE documentation built on Jan. 24, 2020, 1:19 a.m.