rocCurve: Display rate classification performance

Description Usage Arguments Value See Also Examples

Description

Display rate classification performance

A method to visualize the performance in the classification of synthesis, degradation and processing rates based on the comparison of the original simulated rates and the one obtained by the function modelRates. For each rate, classification performance is measured in terms of sensitivity and specificity using a ROC curve analysis. False negatives (FN) represent cases where the rate is identified as constant while it was simulated as varying. False positives (FP) represent cases where INSPEcT identified a rate as varying while it was simulated as constant. On the contrary, true positives (TP) and negatives (TN) are cases of correct classification of varying and constant rates, respectively. Consequently, sensitivity and specificity are computed using increasing thresholds for the brown p-values, and the ability of correctly classifying a rate is measured through the area under the curve (AUC) for each rate.

Usage

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rocCurve(object, object2, cTsh = NULL, plot = TRUE)

## S4 method for signature 'INSPEcT_model,INSPEcT_model'
rocCurve(object, object2, cTsh = NULL,
  plot = TRUE)

## S4 method for signature 'INSPEcT_model,INSPEcT'
rocCurve(object, object2, cTsh = NULL,
  plot = TRUE)

Arguments

object

An object of class INSPEcT_model, with true rates

object2

An object of class INSPEcT or INSPEcT_model, with modeled rates

cTsh

A numeric representing the threshold for the chi-squared test to consider a model as valid; if NULL the value is taken from the INSPEcT_model object

plot

A logical indicating whether ROC curves should be plotted or not

Value

A list of objects of class pROC with summary of each roc curve

See Also

makeSimModel, makeSimDataset, rocThresholds

Examples

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data('nascentInspObj', package='INSPEcT')	

simRates<-makeSimModel(nascentInspObj, 1000, seed=1)
 
newTpts<-simRates@params$tpts
nascentInspObj_sim3<-makeSimDataset(object=simRates
                                   ,tpts=newTpts
                                   ,nRep=3
                                   ,NoNascent=FALSE
                                   ,seed=1)
nascentInspObj_sim3<-modelRates(nascentInspObj_sim3[1:10]
                               ,seed=1)

rocCurve(simRates[1:10],nascentInspObj_sim3)
title("3rep. 11t.p. Total and nascent RNA", line=3)

ste-depo/INSPEcT documentation built on July 30, 2018, 12:04 p.m.