predictClasses-CohortList-PCOSP_or_RLS_or_RGA-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 CohortList Using a PCOSP, RLSModel or RGAModel object.

Usage

## S4 method for signature 'CohortList,PCOSP_or_RLS_or_RGA'
predictClasses(object, model, ...)

Arguments

object	A CohortList with SurvivalExperiments to predict classes for.
model	A trained PCOSP model to use for predicting classes.
...	Fall through arguments to BiocParallel::bplapply for configuring parallelization settings.

Value

A CohortList with the model predictions attached to each SurvivalExperiment in the metadata slot and the prob_good_survival column added to the colData slot.

Examples

data(sampleTrainedPCOSPmodel)
data(sampleCohortList)

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

# Make predictions
PCOSPpredCohortList <- predictClasses(sampleCohortList[seq_len(2)],
  model=sampleTrainedPCOSPmodel)
head(colData(PCOSPpredCohortList[[1]]))

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