rocThresholds: Display rate classification performance with thresholds...

In ste-depo/INSPEcT: Modeling RNA synthesis, processing and degradation with RNA-seq data

Description

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, at increasing brown p-values different sensitivity and specificity can be achieved.

Usage

rocThresholds(object, object2, xlim = c(1e-05, 1), plot = TRUE)

## S4 method for signature 'INSPEcT_model,INSPEcT'
rocThresholds(object, object2, xlim = c(1e-05, 1), 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
xlim	A numeric representing limits for the x-axis (default is c(1-e-5,1))
plot	A logical that indicates whether to plot or not. (default=TRUE)

Value

The thresholds that maximize both sensitivity and specificity

See Also

makeSimModel, makeSimDataset, rocCurve

Examples

if( Sys.info()["sysname"] != "Windows" ) {
  nascentInspObj <- readRDS(system.file(package='INSPEcT', 'nascentInspObj.rds'))
 
  simRates<-makeSimModel(nascentInspObj, 1000, seed=1)
   
  # newTpts<-simRates@params$tpts
  # nascentSim2replicates<-makeSimDataset(object=simRates
  #                                    ,tpts=newTpts
  #                                    ,nRep=3
  #                                    ,NoNascent=FALSE
  #                                    ,seed=1)
  # nascentSim2replicates<-modelRates(nascentSim2replicates[1:100]
  #                                ,seed=1)
  # (not evaluated to save computational time)
 
  data("nascentSim2replicates",package='INSPEcT')
 
  rocThresholds(simRates[1:100],nascentSim2replicates)
}

ste-depo/INSPEcT documentation built on Oct. 3, 2020, 9:14 p.m.