barPlotModelComparison: Make A Bar Plot Comparing Performance Between Two 'S4'...

In bhklab/PDATK: Pancreatic Ductal Adenocarcinoma Tool-Kit

Description

Make A Bar Plot Comparing Performance Between Two S4 Objects Representing Mathematical Models.

Usage

barPlotModelComparison(model1, model2, ...)

Arguments

model1	AnS4 object containing results of a mathematical model
model2	An S4 object containing results of a different mathematical model, but with the same or overlapping samples.
...	Allow new parameters to be defined for this generic.

Value

A bar plot comparing some aspect of model1 and model2

Examples

data(sampleCohortList)
data(sampleValPCOSPmodel)
data(sampleICGCmicro)

# Set parallelization settings
BiocParallel::register(BiocParallel::SerialParam())

# Setup the models
set.seed(1987)
clinicalModel <- ClinicalModel(sampleICGCmicro,
  formula='prognosis ~ sex + age + T + N + M + grade',
  randomSeed=1987)

# Train the models
trainedClinicalModel <- trainModel(clinicalModel)

# Make predctions
clinicalPredCohortList <- predictClasses(sampleCohortList[c('PCSI', 'TCGA')],
  model=trainedClinicalModel)

# Validate the models
validatedClinicalModel <- validateModel(trainedClinicalModel,
  valData=clinicalPredCohortList)

# Plot the comparison
modelCompBarPlot <- barPlotModelComparison(validatedClinicalModel,
 sampleValPCOSPmodel, stat='AUC')

bhklab/PDATK documentation built on Dec. 27, 2021, 7:46 a.m.