validateModel-ClinicalModel-CohortList-method: Evaluate the Performance of a List of Trained KTSP Models...

In bhklab/PDATK: Pancreatic Ductal Adenocarcinoma Tool-Kit

Description

Evaluate the Performance of a List of Trained KTSP Models from a PCOSP Model

Usage

## S4 method for signature 'ClinicalModel,CohortList'
validateModel(model, valData, ...)

Arguments

model	A trained ClinicalModel object, as returned by the trainModel method.
valData	A CohortList containing one or more SurvivalExperiments. The first assay in each SurvivalExperiment will be classified using all top scoring KTSP models in models(model).
...	Fallthrough arguments to BiocParallel::bplapply, use this to configure the parallelization settings for this function. For example to specify BPARAM.

Value

The model object with the validationStats and validationData slots occupied.

See Also

BiocParallel::bplapply, switchBox::SWAP.KTSP.Classify

Examples

data(sampleClinicalModel)
data(samplePCSIsurvExp)

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

# Train Model
trainedClinicalModel <- trainModel(sampleClinicalModel)

# Make predictions
clinicalPredSurvExp <- predictClasses(samplePCSIsurvExp,
  model=trainedClinicalModel)

# Validate model
validatedClincalModel <- validateModel(trainedClinicalModel,
  valData=clinicalPredSurvExp)

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