predictClasses-SurvivalExperiment-ClinicalModel-method: Predict Survival Prognosis Classes and Risk Scores for A...

In bhklab/PDATK: Pancreatic Ductal Adenocarcinoma Tool-Kit

Description

Predict Survival Prognosis Classes and Risk Scores for A SurvivalModel Using a ClinicalModel Object.

Usage

## S4 method for signature 'SurvivalExperiment,ClinicalModel'
predictClasses(object, model, ..., na.action = "na.exclude", type = "response")

Arguments

object	A SurvivalExperiment object with the correct columns in colData to match the formula for the ClinicalModel object.
model	A trained ClinicalModel object, as return by trainModel.
...	Fall through parameters to stats::predict.
na.action	The na.action paramter passed to stats::predict.glm.
type	The type parameter passed to stats::predict.glm

Value

A SurvivalExperiment with the model predictions in the colData slot as clinical_prob_good.

Examples

data(sampleClinicalModel)
data(samplePCSIsurvExp)

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

# Train Model
trainedClinicalModel <- trainModel(sampleClinicalModel)

# Make predictions
ClinicalPredSurvExp <- predictClasses(samplePCSIsurvExp,
  model=trainedClinicalModel)
head(colData(ClinicalPredSurvExp))

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