Package org.biojava.nbio.survival.cox

Class CoxHelper

java.lang.Object
org.biojava.nbio.survival.cox.CoxHelper
public class CoxHelper extends Object
The CoxHelper class is provided to start with a tab delimited file in a similar process in R and return the results as a CoxInfo class. Given the number of options for adjusting the calculations using weighting, strata, clustering etc the helper class can be used to hide the complexity for typical use case.
Author:
Scooter Willis

  • Constructor Details

    • CoxHelper

      public CoxHelper()

  • Method Details

    • process

      public static CoxInfo process(String datafile, String timeColumn, String statusColumn, String weightColumn, String strataColumn, String clusterColumn, ArrayList<String> variables, boolean useStrata, boolean useWeights) throws Exception
      Parameters:
      datafile - The tab delimited file containing survival data and variables. The first column needs to be unique index
      timeColumn - The column representing the event/censor time
      statusColumn - The column representing an event=1 and censor=0
      weightColumn - For case-cohort data sets may require weighting to reflect the entire cohort
      strataColumn - A column representing strata data
      clusterColumn - If robost variation calculation is required the cluster column will group samples by the value in this column
      variables - The variables to be used in the cox regression analysis. For Interactions using variable1:variable2
      useStrata - Boolean to indicate if strata column should be used
      useWeights - Boolean to indicate if weight column should be used
      Returns:
      Throws:
      Exception

    • process

      public static CoxInfo process(WorkSheet worksheet, String timeColumn, String statusColumn, String weightColumn, String strataColumn, String clusterColumn, ArrayList<String> variables, boolean useStrata, boolean useWeights)
      Parameters:
      worksheet -
      timeColumn - The column representing the event/censor time
      statusColumn - The column representing an event=1 and censor=0
      weightColumn - For case-cohort data sets may require weighting to reflect the entire cohort
      strataColumn - A column representing strata data
      clusterColumn - If robost variation calculation is required the cluster column will group samples by the value in this column
      variables - The variables to be used in the cox regression analysis. For Interactions using variable1:variable2
      useStrata - Boolean to indicate if strata column should be used
      useWeights - Boolean to indicate if weight column should be used
      Returns:

    • main

      public static void main(String[] args)
      Parameters:
      args - the command line arguments