predictClasses,CohortList,ClinicalModel-method {PDATK} | R Documentation |
CohortList
of
SurvivalExperment
Objects.Use a Clinical GLM to Predict Classes for a CohortList
of
SurvivalExperment
Objects.
## S4 method for signature 'CohortList,ClinicalModel' predictClasses(object, model, ..., na.action = "na.exclude", type = "response")
object |
A |
model |
A trained |
... |
Fall through parameters to |
na.action |
The |
type |
The |
A CohortList
with the model predictions in the colData
slot as clinical_prob_good for each SurvivalExperiment
, and the
model in the metadata as predictionModel.
data(sampleClinicalModel) data(sampleCohortList) # Set parallelization settings BiocParallel::register(BiocParallel::SerialParam()) # Train Model trainedClinicalModel <- trainModel(sampleClinicalModel) # Make predictions ClinicalPredCohortList <- predictClasses(sampleCohortList[c('PCSI', 'TCGA')], model=trainedClinicalModel) head(colData(ClinicalPredCohortList[[1]]))