fitCoxPH: Fit coxph model with a predictor variable and a set of...
In marioni-group/MethylPipeR: MethylPipeR

fitCoxPH

R Documentation

Fit coxph model with a predictor variable and a set of covariates.

Description

Fit coxph model with a predictor variable and a set of covariates.

Usage

fitCoxPH(
  modelPredictions,
  targetTable,
  covariatesTable,
  covariateColnames,
  pipelineRunInformation,
  modelLabel
)

Arguments

`modelPredictions`	A vector of model predictions.
`targetTable`	A matrix/data.frame with columns named 'Event' and 'time_to_event'. 'Event' should correspond to a binary label. 'time_to_event' should correspond to a positive numerical value representing the survival time (when Event == 1) or the time-to-censoring (when Event == 0)
`covariatesTable`	A table that includes columns corresponding to covariates to be included in the model.
`covariateColnames`	A named list with names corresponding to the covariate column names to be used in the model. The values in the list should correspond to the actual column name in `covariatesTable`
`pipelineRunInformation`	The object originally created by `beginPipelineRun`.
`modelLabel`	A string that will act as a label for this function call. The label will be used as a prefix for the saved object filenames in this function call.

Value

A named list consisting of the following elements: 'coxPHModel' is the fit coxph model object (from the survival library). 'coxPHModelSummary' is the result from calling summary() on coxPHModel. 'pseudoR2' is the pseudo r-squared value for the model. 'hazardRatio' is the hazard ratio for the predictor variable.