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

In bhklab/PanCuRx: 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 'SurvivalExperiment,PCOSP_or_RLS_or_RGA'
predictClasses(object, model, ...)

Arguments

object	A SurvivalExperiment object 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 SurvivalExperiment with the predictions in its metadata and a column in colData, prob_good_survival, which contains the proportion of models which predicted good prognosis for each sample.

See Also

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

Examples

data(sampleTrainedPCOSPmodel)
data(samplePCSIsurvExp)

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

# Make predictions
PCOSPpredSurvExp <- predictClasses(samplePCSIsurvExp,
  model=sampleTrainedPCOSPmodel)
head(colData(PCOSPpredSurvExp))

bhklab/PanCuRx documentation built on Dec. 30, 2021, 4:59 p.m.