Description Usage Arguments Value Examples
Use a Clinical GLM to Predict Classes for a CohortList
of
SurvivalExperment
Objects.
1 2 | ## 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.
1 2 3 4 5 6 7 8 9 10 11 12 13 | 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]]))
|
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