CoxModel: CoxModel constructor

In bhklab/PDATK: Pancreatic Ductal Adenocarcinoma Tool-Kit

Description

Build a CoxModel object from a MultiAssayExperiment of SurvivalExperiments. Allows easy application of the survival::coxph function to many SurvivalExperiment at once, assuming they share the survivalPredictor column.

Usage

CoxModel(object, survivalPredictor = "metacluster_labels")

Arguments

object	A MultiAssayExperiment containing only SurvivalExperiment objects.
survivalPredictor	A character vector indicating the name of the one or more columns in the colData slot of each SurvivalExperiment to use for testing survival differences between different groups. Must be a valid column in the colData of ALL experiments.

Value

A CoxModel object, with object in the trainData slot.

Examples

library(MultiAssayExperiment)
data(CSPC_MAE)
experiments(CSPC_MAE) <- endoapply(experiments(CSPC_MAE), SurvivalExperiment,
    event_occurred='vital_status', survival_time='days_to_death')
coxModel <- CoxModel(CSPC_MAE, survivalPredictor='sample_type')

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